initial commit

.eslintrc.js

+module.exports = {
+	"env" : {
+		"browser" : true,
+		"jquery" : true,
+		"es6" : true,
+		"worker" : true
+	},
+	"extends" : "eslint:recommended",
+	"rules" : {
+		"indent" : [ "error", "tab" ],
+		"linebreak-style" : [ "error", "unix" ],
+		"quotes" : [ "error", "single" ],
+		"semi" : [ "error", "always" ],
+		"no-redeclare" : 0,
+		"no-console" : 0
+	},
+	"globals" : {
+		"morpheus" : true,
+		"_" : true,
+		"d3" : true,
+		"Plotly" : true,
+		"colorbrewer" : true,
+		"Hammer" : true,
+		"XLSX" : true,
+		"canvg" : true,
+		"Clipboard" : true,
+		"Newick" : true,
+		"saveAs" : true,
+		"Slick" : true,
+		"C2S" : true
+	}
+};
\ No newline at end of file

.gitignore

+node_modules
+.project
+.settings
+morpheus_3rd_party.xlsx
+js/morpheus-external.js
+js/morpheus-external.min.js
+js/morpheus.js
\ No newline at end of file

Gruntfile.js

+/*global module:false*/
+module.exports = function(grunt) {
+	grunt
+			.initConfig({
+				pkg : grunt.file.readJSON('package.json'),
+				meta : {
+					banner : '/*! <%= pkg.title || pkg.name %> - v<%= pkg.version %> - '
+							+ '<%= grunt.template.today("yyyy-mm-dd") %>\n'
+							+ '<%= pkg.homepage ? "* " + pkg.homepage + "\n" : "" %>'
+							+ '* Copyright (c) <%= grunt.template.today("yyyy") %> <%= pkg.author.name %>; %> */'
+				},
+				uglify : {
+					morpheus : {
+						options : {
+							mangle : false,
+							preserveComments : false
+						},
+						files : {
+							'js/morpheus-latest.min.js' : [ 'js/morpheus.js' ]
+						}
+					},
+					extJs : {
+						options : {
+							mangle : false,
+							preserveComments : false
+						},
+						files : {
+							'js/morpheus-external.min.js' : [ 'js/morpheus-external.js' ]
+						}
+					}
+				},
+				cssmin : {
+					css : {
+						src : 'css/morpheus.all.css',
+						dest : 'css/morpheus-latest.min.css'
+					}
+				},
+				concat : {
+					css : {
+						src : [ 'css/bootstrap.min.css',
+								'css/bootstrap-select.min.css',
+								'css/jquery-ui.min.css',
+								'css/font-awesome.min.css',
+								'css/hopscotch.min.css', 'css/slick.grid.css',
+								'css/animate.css', 'css/morpheus.css' ],
+						dest : 'css/morpheus.all.css'
+					},
+					extJsAll : {
+						src : [ 'js/morpheus-external.min.js',
+								'js/plotly-latest.min.js' ],
+						dest : 'js/morpheus-external-latest.min.js'
+					},
+					extJs : {
+						nonull : true,
+						dest : 'js/morpheus-external.js',
+						src : [ 'js/d3.min.js', 'js/jquery-1.11.1.min.js',
+								'js/bootstrap.min.js', 'js/underscore-min.js',
+								'js/newick.js', 'js/hammer.min.js',
+								'js/jquery.mousewheel.min.js',
+								'js/bootstrap-select.min.js',
+								'js/xlsx.full.min.js', 'js/canvas2svg.js',
+								'js/canvg.js', 'js/rgbcolor.js',
+								'js/jquery-ui.min.js', 'js/parser.js',
+								'js/FileSaver.min.js', 'js/Blob.js',
+								'js/canvas-toBlob.js', 'js/colorbrewer.js',
+								'js/hopscotch.min.js', 'js/typed.min.js',
+								'js/jquery.event.drag-2.2.js',
+								'js/clipboard.min.js', 'js/slick.min.js',
+								'js/js.cookie.js', 'js/d3.layout.cloud.js' ]
+					},
+					morpheus : {
+						nonull : true,
+						dest : 'js/morpheus.js',
+						src : [ 'src/util/util.js', 'src/util/*.js',
+								'src/io/*.js', 'src/matrix/vector_adapter.js',
+								'src/matrix/*.js', 'src/*.js',
+								'src/tools/*.js', 'src/ui/list.js',
+								'src/ui/*.js', 'src/**/*.js' ]
+					}
+				},
+				watch : {
+					files : [ 'src/*.js', 'src/**/*.js' ],
+					tasks : [ 'concat:morpheus' ]
+				}
+			});
+	grunt.registerTask('default', 'watch');
+	grunt.loadNpmTasks('grunt-contrib-watch');
+	grunt.loadNpmTasks('grunt-contrib-concat');
+	grunt.loadNpmTasks('grunt-contrib-uglify');
+	grunt.loadNpmTasks('grunt-contrib-copy');
+	grunt.loadNpmTasks('grunt-contrib-cssmin');
+	grunt.loadNpmTasks('grunt-contrib-jshint');
+};

css/bootstrap-select.min.css

+/*!
+ * Bootstrap-select v1.9.4 (http://silviomoreto.github.io/bootstrap-select)
+ *
+ * Copyright 2013-2016 bootstrap-select
+ * Licensed under MIT (https://github.com/silviomoreto/bootstrap-select/blob/master/LICENSE)
+ */.bootstrap-select{width:220px\9}.bootstrap-select>.dropdown-toggle{width:100%;padding-right:25px;z-index:1}.bootstrap-select>select{position:absolute!important;bottom:0;left:50%;width:.11px!important;height:100%!important;padding:0!important;opacity:0!important;border:none}.bootstrap-select>select.mobile-device{top:0;left:0;display:block!important;width:100%!important;z-index:2}.error .bootstrap-select .dropdown-toggle,.has-error .bootstrap-select .dropdown-toggle{border-color:#b94a48}.bootstrap-select.fit-width{width:auto!important}.bootstrap-select:not([class*=col-]):not([class*=form-control]):not(.input-group-btn){width:220px}.bootstrap-select .dropdown-toggle:focus{outline:thin dotted #333!important;outline:5px auto -webkit-focus-ring-color!important;outline-offset:-2px}.bootstrap-select.form-control{margin-bottom:0;padding:0;border:none}.bootstrap-select.form-control:not([class*=col-]){width:100%}.bootstrap-select.form-control.input-group-btn{z-index:auto}.bootstrap-select.btn-group:not(.input-group-btn),.bootstrap-select.btn-group[class*=col-]{float:none;display:inline-block;margin-left:0}.bootstrap-select.btn-group.dropdown-menu-right,.bootstrap-select.btn-group[class*=col-].dropdown-menu-right,.row .bootstrap-select.btn-group[class*=col-].dropdown-menu-right{float:right}.form-group .bootstrap-select.btn-group,.form-horizontal .bootstrap-select.btn-group,.form-inline .bootstrap-select.btn-group{margin-bottom:0}.form-group-lg .bootstrap-select.btn-group.form-control,.form-group-sm .bootstrap-select.btn-group.form-control{padding:0}.form-inline .bootstrap-select.btn-group .form-control{width:100%}.bootstrap-select.btn-group.disabled,.bootstrap-select.btn-group>.disabled{cursor:not-allowed}.bootstrap-select.btn-group.disabled:focus,.bootstrap-select.btn-group>.disabled:focus{outline:0!important}.bootstrap-select.btn-group.bs-container{position:absolute}.bootstrap-select.btn-group.bs-container .dropdown-menu{z-index:1060}.bootstrap-select.btn-group .dropdown-toggle .filter-option{display:inline-block;overflow:hidden;width:100%;text-align:left}.bootstrap-select.btn-group .dropdown-toggle .caret{position:absolute;top:50%;right:12px;margin-top:-2px;vertical-align:middle}.bootstrap-select.btn-group[class*=col-] .dropdown-toggle{width:100%}.bootstrap-select.btn-group .dropdown-menu{min-width:100%;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}.bootstrap-select.btn-group .dropdown-menu.inner{position:static;float:none;border:0;padding:0;margin:0;border-radius:0;-webkit-box-shadow:none;box-shadow:none}.bootstrap-select.btn-group .dropdown-menu li{position:relative}.bootstrap-select.btn-group .dropdown-menu li.active small{color:#fff}.bootstrap-select.btn-group .dropdown-menu li.disabled a{cursor:not-allowed}.bootstrap-select.btn-group .dropdown-menu li a{cursor:pointer;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none}.bootstrap-select.btn-group .dropdown-menu li a.opt{position:relative;padding-left:2.25em}.bootstrap-select.btn-group .dropdown-menu li a span.check-mark{display:none}.bootstrap-select.btn-group .dropdown-menu li a span.text{display:inline-block}.bootstrap-select.btn-group .dropdown-menu li small{padding-left:.5em}.bootstrap-select.btn-group .dropdown-menu .notify{position:absolute;bottom:5px;width:96%;margin:0 2%;min-height:26px;padding:3px 5px;background:#f5f5f5;border:1px solid #e3e3e3;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.05);box-shadow:inset 0 1px 1px rgba(0,0,0,.05);pointer-events:none;opacity:.9;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}.bootstrap-select.btn-group .no-results{padding:3px;background:#f5f5f5;margin:0 5px;white-space:nowrap}.bootstrap-select.btn-group.fit-width .dropdown-toggle .filter-option{position:static}.bootstrap-select.btn-group.fit-width .dropdown-toggle .caret{position:static;top:auto;margin-top:-1px}.bootstrap-select.btn-group.show-tick .dropdown-menu li.selected a span.check-mark{position:absolute;display:inline-block;right:15px;margin-top:5px}.bootstrap-select.btn-group.show-tick .dropdown-menu li a span.text{margin-right:34px}.bootstrap-select.show-menu-arrow.open>.dropdown-toggle{z-index:1061}.bootstrap-select.show-menu-arrow .dropdown-toggle:before{content:'';border-left:7px solid transparent;border-right:7px solid transparent;border-bottom:7px solid rgba(204,204,204,.2);position:absolute;bottom:-4px;left:9px;display:none}.bootstrap-select.show-menu-arrow .dropdown-toggle:after{content:'';border-left:6px solid transparent;border-right:6px solid transparent;border-bottom:6px solid #fff;position:absolute;bottom:-4px;left:10px;display:none}.bootstrap-select.show-menu-arrow.dropup .dropdown-toggle:before{bottom:auto;top:-3px;border-top:7px solid rgba(204,204,204,.2);border-bottom:0}.bootstrap-select.show-menu-arrow.dropup .dropdown-toggle:after{bottom:auto;top:-3px;border-top:6px solid #fff;border-bottom:0}.bootstrap-select.show-menu-arrow.pull-right .dropdown-toggle:before{right:12px;left:auto}.bootstrap-select.show-menu-arrow.pull-right .dropdown-toggle:after{right:13px;left:auto}.bootstrap-select.show-menu-arrow.open>.dropdown-toggle:after,.bootstrap-select.show-menu-arrow.open>.dropdown-toggle:before{display:block}.bs-actionsbox,.bs-donebutton,.bs-searchbox{padding:4px 8px}.bs-actionsbox{width:100%;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}.bs-actionsbox .btn-group button{width:50%}.bs-donebutton{float:left;width:100%;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box}.bs-donebutton .btn-group button{width:100%}.bs-searchbox+.bs-actionsbox{padding:0 8px 4px}.bs-searchbox .form-control{margin-bottom:0;width:100%;float:none}
\ No newline at end of file

css/morpheus.css

+.morpheus-sep {
+	border-top: 1px solid #eee;
+}
+
+.dropdown-checkbox {
+	margin-left: -16px !important;
+}
+
+.ui-dialog .ui-dialog-titlebar {
+	font-size: 12px !important;
+	padding: 0.1em 1em !important;
+	background: black !important;
+}
+
+.axis path, .axis line {
+	fill: none;
+	stroke: #000;
+	shape-rendering: crispEdges;
+}
+
+.select2-search-choice {
+	background: white !important;
+}
+
+.select2-search-choice:hover {
+	background: rgb(230, 230, 230) !important;
+}
+
+.ui-autocomplete {
+	max-height: 200px;
+	overflow-y: auto;
+	/* prevent horizontal scrollbar */
+	overflow-x: hidden;
+}
+
+.morpheus-button-divider {
+	width: 6px;
+	display: inline-block;
+}
+
+.morpheus-hover-show {
+	display: none !important;
+}
+
+.morpheus-hover:hover>.morpheus-hover-show {
+	display: block !important;
+}
+
+.morpheus-hover:hover {
+	background-color: #f5f5f5;
+}
+
+.morpheus-tip {
+	font-size: 12px;
+	position: absolute;
+	top: 0;
+	left: 0;
+	min-height: 24px;
+	max-height: 24px;
+	height: 24px;
+	line-height: 1;
+	color: #777;
+}
+
+.morpheus-tip-inline {
+	font-size: 12px;
+	max-width: 400px;
+	z-index: 10000;
+	position: absolute;
+	background-color: rgba(255, 255, 255, 0.9);
+	color: black;
+	text-align: left;
+	padding-left: 10px;
+	padding-right: 10px;
+	box-shadow: rgba(0, 0, 0, 0.498039) 0px 5px 15px;
+	border: 1px solid rgba(0, 0, 0, 0.2);
+	border-radius: 6px;
+	overflow: hidden;
+}
+
+.morpheus-form-control-inline {
+	display: inline !important;
+	width: auto !important;
+	margin-right: 1em !important;
+}
+
+.morpheus-tip-dialog {
+	font-size: 12px !important;
+	color: #777 ! important;
+	padding: 2px !important;
+	background-color: white !important;
+}
+
+.slick-cell {
+	margin: 0px;
+	border: none;
+	padding: 0px;
+	background-color: inherit;
+}
+
+.slick-row {
+	font-size: 13px;
+	line-height: 100%;
+	padding: 0px;
+	margin: 0px;
+}
+
+.slick-header-column.ui-state-default {
+	height: 20px;
+	line-height: 20px;
+	padding: 0px;
+	background: none;
+	background-color: #f6f7f8;
+}
+
+.slick-header-columns {
+	background-color: white;
+}
+
+.slick-table .ui-widget-content {
+	background: none;
+}
+
+.slick-table-compact .slick-row {
+	font-size: 12px;
+}
+
+.slick-table .slick-row {
+	background-color: white;
+}
+
+.slick-striped-table .slick-row.odd {
+	background-color: #fafafa;
+}
+
+.slick-header-column {
+	color: black;
+	background-color: white;
+	font-weight: bold;
+	border-left: 1px solid black;
+}
+
+.slick-cell, .slick-headerrow-column {
+	overflow: hidden;
+	text-overflow: ellipsis;
+}
+
+.slick-header {
+	background-color: white;
+	border: none !important;
+}
+
+.slick-cell.selected {
+	background-color: #d9edf7;
+}
+
+.slick-stacked .slick-visible-stacked {
+	display: block;
+}
+
+.slick-table:not(.slick-stacked) .slick-visible-not-stacked {
+	display: block;
+}
+
+.slick-visible-not-stacked {
+	display: none;
+}
+
+.slick-visible-stacked {
+	display: none;
+}
+
+.slick-sort-indicator-desc {
+	background: none;
+}
+
+.slick-sort-indicator-asc {
+	background: none;
+}
+
+.slick-sort-indicator-desc::after {
+	content: "\f0dd";
+	font-family: FontAwesome;
+	margin-right: 3px;
+	margin-left: 4px;
+	margin-top: -3px;
+}
+
+.slick-sort-indicator {
+	float: none !important;
+	margin: 0 !important;
+}
+
+.slick-header-column-sorted {
+	font-style: normal;
+}
+
+.slick-column-name {
+	margin-left: 4px;
+}
+
+.slick-sort-indicator-asc::after {
+	content: "\f0de";
+	font-family: FontAwesome;
+	margin-right: 3px;
+	margin-left: 4px;
+	margin-top: -3px;
+	float: none;
+}
\ No newline at end of file

css/slick.grid.css

+/*
+IMPORTANT:
+In order to preserve the uniform grid appearance, all cell styles need to have padding, margin and border sizes.
+No built-in (selected, editable, highlight, flashing, invalid, loading, :focus) or user-specified CSS
+classes should alter those!
+*/
+.slick-header.ui-state-default, .slick-headerrow.ui-state-default {
+	width: 100%;
+	overflow: hidden;
+	border-left: 0px;
+}
+
+.slick-header-columns, .slick-headerrow-columns {
+	position: relative;
+	white-space: nowrap;
+	cursor: default;
+	overflow: hidden;
+}
+
+.slick-header-column.ui-state-default {
+	position: relative;
+	display: inline-block;
+	overflow: hidden;
+	-o-text-overflow: ellipsis;
+	text-overflow: ellipsis;
+	height: 16px;
+	line-height: 16px;
+	margin: 0;
+	padding: 4px;
+	border-right: 1px solid silver;
+	border-left: 0px;
+	border-top: 0px;
+	border-bottom: 0px;
+	float: left;
+}
+
+.slick-headerrow-column.ui-state-default {
+	padding: 4px;
+}
+
+.slick-header-column-sorted {
+	font-style: italic;
+}
+
+.slick-sort-indicator {
+	display: inline-block;
+	width: 8px;
+	height: 5px;
+	margin-left: 4px;
+	margin-top: 6px;
+	float: left;
+}
+
+.slick-sort-indicator-desc {
+	background: url(images/sort-desc.gif);
+}
+
+.slick-sort-indicator-asc {
+	background: url(images/sort-asc.gif);
+}
+
+.slick-resizable-handle {
+	position: absolute;
+	font-size: 0.1px;
+	display: block;
+	cursor: col-resize;
+	width: 4px;
+	right: 0px;
+	top: 0;
+	height: 100%;
+}
+
+.slick-sortable-placeholder {
+	background: silver;
+}
+
+.grid-canvas {
+	position: relative;
+	outline: 0;
+}
+
+.slick-row.ui-widget-content, .slick-row.ui-state-active {
+	position: absolute;
+	border: 0px;
+	width: 100%;
+}
+
+.slick-cell, .slick-headerrow-column {
+	position: absolute;
+	border: 1px solid transparent;
+	border-right: 1px dotted silver;
+	border-bottom-color: silver;
+	overflow: hidden;
+	-o-text-overflow: ellipsis;
+	text-overflow: ellipsis;
+	vertical-align: middle;
+	z-index: 1;
+	padding: 1px 2px 2px 1px;
+	margin: 0;
+	white-space: nowrap;
+	cursor: default;
+}
+
+.slick-group {
+	
+}
+
+.slick-group-toggle {
+	display: inline-block;
+}
+
+.slick-cell.highlighted {
+	background: lightskyblue;
+	background: rgba(0, 0, 255, 0.2);
+	-webkit-transition: all 0.5s;
+	-moz-transition: all 0.5s;
+	-o-transition: all 0.5s;
+	transition: all 0.5s;
+}
+
+.slick-cell.flashing {
+	border: 1px solid red !important;
+}
+
+.slick-cell.editable {
+	z-index: 11;
+	overflow: visible;
+	background: white;
+	border-color: black;
+	border-style: solid;
+}
+
+.slick-cell:focus {
+	outline: none;
+}
+
+.slick-reorder-proxy {
+	display: inline-block;
+	background: blue;
+	opacity: 0.15;
+	filter: alpha(opacity = 15);
+	cursor: move;
+}
+
+.slick-reorder-guide {
+	display: inline-block;
+	height: 2px;
+	background: blue;
+	opacity: 0.7;
+	filter: alpha(opacity = 70);
+}
+
+.slick-selection {
+	z-index: 10;
+	position: absolute;
+	border: 2px dashed black;
+}
\ No newline at end of file

images/icon.svg

+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   width="32px"
+   height="32px"
+   version="1.1">
+  <g>
+      <rect
+         x="0"
+         y="0"
+         width="32"
+         height="14"
+         style="fill:#ca0020;stroke:none" />
+      <rect
+         x="0"
+         y="18"
+         width="32"
+         height="14"
+         style="fill:#0571b0;stroke:none" />
+     
+  </g>
+</svg>

index.html

+<!DOCTYPE html>
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport"
+	content="user-scalable=no, width=device-width, initial-scale=1, maximum-scale=1">
+<meta name="google-site-verification"
+	content="7UY7VcXR28Tpmw6m6fc6wtJJQvar71GKqGojp3HPb4Q" />
+<title>Morpheus</title>
+<script type="text/javascript" src="js/morpheus-external-latest.min.js"></script>
+<script src="js/morpheus-latest.min.js"></script>
+<script src="js/jsme/jsme.nocache.js"></script>
+<link rel="stylesheet" href="css/morpheus-latest.min.css">
+<link
+	href="https://fonts.googleapis.com/css?family=Roboto' rel='stylesheet"
+	type="text/css">
+<link rel="shortcut icon" href="favicon.ico" type="image/x-icon">
+<script type="text/javascript"
+	src="https://www.dropbox.com/static/api/2/dropins.js" id="dropboxjs"
+	data-app-key="6xq3zgeoago5fhw"></script>
+</head>
+<body>
+	<noscript>
+		<p>Please enable JavaScript</p>
+	</noscript>
+	<div style="width: 100%; height: auto;" id="vis"></div>
+
+	<script type="text/javascript">
+		window.onerror = function() {
+			morpheus.FormBuilder.showInModal({
+				title : 'Error',
+				html : 'Oops, soomething went wrong. Please try again.'
+			});
+		};
+
+		var landingPage = new morpheus.LandingPage();
+		landingPage.$el.prependTo($(document.body));
+		if (window.location.search.length === 0) {
+			landingPage.show();
+		} else {
+			var search = window.location.search.substring(1);
+			var keyValuePairs = search.split('&');
+			var params = {};
+			for (var i = 0; i < keyValuePairs.length; i++) {
+				var pair = keyValuePairs[i].split('=');
+				params[pair[0]] = decodeURIComponent(pair[1]);
+			}
+			if (params.json) {
+				var options = JSON.parse(params.json);
+				landingPage.open(options);
+			} else if (params.url) { // url to config
+				$.ajax({
+					url : params.url
+				}).done(function(json) {
+					landingPage.open(json);
+				}).fail(function() {
+					console.log('Unable to get config file');
+					landingPage.show();
+				});
+			} else {
+				landingPage.show();
+			}
+		}
+	</script>
+
+</body>
+</html>
+

jasmine/SpecRunner.html

+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="utf-8">
+<title>Morpheus Test - Jasmine Spec Runner v2.4.1</title>
+
+<link rel="shortcut icon" type="image/png"
+	href="lib/jasmine-2.4.1/jasmine_favicon.png">
+<link rel="stylesheet" href="lib/jasmine-2.4.1/jasmine.css">
+
+<script src="lib/jasmine-2.4.1/jasmine.js"></script>
+<script src="lib/jasmine-2.4.1/jasmine-html.js"></script>
+<script src="lib/jasmine-2.4.1/boot.js"></script>
+
+<!-- include source files here... -->
+<script src="../js/morpheus.external.min.js"></script>
+<script src="../js/morpheus.js"></script>
+
+<!-- include spec files here... -->
+<script src="matchers/custom.js"></script>
+<script src="spec/univariate_functions_test.js"></script>
+<script src="spec/bivariate_functions_test.js"></script>
+<script src="spec/dataset_test.js"></script>
+<script src="spec/set_test.js"></script>
+<script src="spec/ranking_test.js"></script>
+<script src="spec/adjust_tool_test.js"></script>
+</head>
+<body>
+</body>
+</html>

jasmine/lib/jasmine-2.4.1/boot.js

+/**
+ Starting with version 2.0, this file "boots" Jasmine, performing all of the necessary initialization before executing the loaded environment and all of a project's specs. This file should be loaded after `jasmine.js` and `jasmine_html.js`, but before any project source files or spec files are loaded. Thus this file can also be used to customize Jasmine for a project.
+
+ If a project is using Jasmine via the standalone distribution, this file can be customized directly. If a project is using Jasmine via the [Ruby gem][jasmine-gem], this file can be copied into the support directory via `jasmine copy_boot_js`. Other environments (e.g., Python) will have different mechanisms.
+
+ The location of `boot.js` can be specified and/or overridden in `jasmine.yml`.
+
+ [jasmine-gem]: http://github.com/pivotal/jasmine-gem
+ */
+
+(function() {
+
+  /**
+   * ## Require & Instantiate
+   *
+   * Require Jasmine's core files. Specifically, this requires and attaches all of Jasmine's code to the `jasmine` reference.
+   */
+  window.jasmine = jasmineRequire.core(jasmineRequire);
+
+  /**
+   * Since this is being run in a browser and the results should populate to an HTML page, require the HTML-specific Jasmine code, injecting the same reference.
+   */
+  jasmineRequire.html(jasmine);
+
+  /**
+   * Create the Jasmine environment. This is used to run all specs in a project.
+   */
+  var env = jasmine.getEnv();
+
+  /**
+   * ## The Global Interface
+   *
+   * Build up the functions that will be exposed as the Jasmine public interface. A project can customize, rename or alias any of these functions as desired, provided the implementation remains unchanged.
+   */
+  var jasmineInterface = jasmineRequire.interface(jasmine, env);
+
+  /**
+   * Add all of the Jasmine global/public interface to the global scope, so a project can use the public interface directly. For example, calling `describe` in specs instead of `jasmine.getEnv().describe`.
+   */
+  extend(window, jasmineInterface);
+
+  /**
+   * ## Runner Parameters
+   *
+   * More browser specific code - wrap the query string in an object and to allow for getting/setting parameters from the runner user interface.
+   */
+
+  var queryString = new jasmine.QueryString({
+    getWindowLocation: function() { return window.location; }
+  });
+
+  var catchingExceptions = queryString.getParam("catch");
+  env.catchExceptions(typeof catchingExceptions === "undefined" ? true : catchingExceptions);
+
+  var throwingExpectationFailures = queryString.getParam("throwFailures");
+  env.throwOnExpectationFailure(throwingExpectationFailures);
+
+  var random = queryString.getParam("random");
+  env.randomizeTests(random);
+
+  var seed = queryString.getParam("seed");
+  if (seed) {
+    env.seed(seed);
+  }
+
+  /**
+   * ## Reporters
+   * The `HtmlReporter` builds all of the HTML UI for the runner page. This reporter paints the dots, stars, and x's for specs, as well as all spec names and all failures (if any).
+   */
+  var htmlReporter = new jasmine.HtmlReporter({
+    env: env,
+    onRaiseExceptionsClick: function() { queryString.navigateWithNewParam("catch", !env.catchingExceptions()); },
+    onThrowExpectationsClick: function() { queryString.navigateWithNewParam("throwFailures", !env.throwingExpectationFailures()); },
+    onRandomClick: function() { queryString.navigateWithNewParam("random", !env.randomTests()); },
+    addToExistingQueryString: function(key, value) { return queryString.fullStringWithNewParam(key, value); },
+    getContainer: function() { return document.body; },
+    createElement: function() { return document.createElement.apply(document, arguments); },
+    createTextNode: function() { return document.createTextNode.apply(document, arguments); },
+    timer: new jasmine.Timer()
+  });
+
+  /**
+   * The `jsApiReporter` also receives spec results, and is used by any environment that needs to extract the results  from JavaScript.
+   */
+  env.addReporter(jasmineInterface.jsApiReporter);
+  env.addReporter(htmlReporter);
+
+  /**
+   * Filter which specs will be run by matching the start of the full name against the `spec` query param.
+   */
+  var specFilter = new jasmine.HtmlSpecFilter({
+    filterString: function() { return queryString.getParam("spec"); }
+  });
+
+  env.specFilter = function(spec) {
+    return specFilter.matches(spec.getFullName());
+  };
+
+  /**
+   * Setting up timing functions to be able to be overridden. Certain browsers (Safari, IE 8, phantomjs) require this hack.
+   */
+  window.setTimeout = window.setTimeout;
+  window.setInterval = window.setInterval;
+  window.clearTimeout = window.clearTimeout;
+  window.clearInterval = window.clearInterval;
+
+  /**
+   * ## Execution
+   *
+   * Replace the browser window's `onload`, ensure it's called, and then run all of the loaded specs. This includes initializing the `HtmlReporter` instance and then executing the loaded Jasmine environment. All of this will happen after all of the specs are loaded.
+   */
+  var currentWindowOnload = window.onload;
+
+  window.onload = function() {
+    if (currentWindowOnload) {
+      currentWindowOnload();
+    }
+    htmlReporter.initialize();
+    env.execute();
+  };
+
+  /**
+   * Helper function for readability above.
+   */
+  function extend(destination, source) {
+    for (var property in source) destination[property] = source[property];
+    return destination;
+  }
+
+}());

jasmine/lib/jasmine-2.4.1/console.js

+/*
+Copyright (c) 2008-2015 Pivotal Labs
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+function getJasmineRequireObj() {
+  if (typeof module !== 'undefined' && module.exports) {
+    return exports;
+  } else {
+    window.jasmineRequire = window.jasmineRequire || {};
+    return window.jasmineRequire;
+  }
+}
+
+getJasmineRequireObj().console = function(jRequire, j$) {
+  j$.ConsoleReporter = jRequire.ConsoleReporter();
+};
+
+getJasmineRequireObj().ConsoleReporter = function() {
+
+  var noopTimer = {
+    start: function(){},
+    elapsed: function(){ return 0; }
+  };
+
+  function ConsoleReporter(options) {
+    var print = options.print,
+      showColors = options.showColors || false,
+      onComplete = options.onComplete || function() {},
+      timer = options.timer || noopTimer,
+      specCount,
+      failureCount,
+      failedSpecs = [],
+      pendingCount,
+      ansi = {
+        green: '\x1B[32m',
+        red: '\x1B[31m',
+        yellow: '\x1B[33m',
+        none: '\x1B[0m'
+      },
+      failedSuites = [];
+
+    print('ConsoleReporter is deprecated and will be removed in a future version.');
+
+    this.jasmineStarted = function() {
+      specCount = 0;
+      failureCount = 0;
+      pendingCount = 0;
+      print('Started');
+      printNewline();
+      timer.start();
+    };
+
+    this.jasmineDone = function() {
+      printNewline();
+      for (var i = 0; i < failedSpecs.length; i++) {
+        specFailureDetails(failedSpecs[i]);
+      }
+
+      if(specCount > 0) {
+        printNewline();
+
+        var specCounts = specCount + ' ' + plural('spec', specCount) + ', ' +
+          failureCount + ' ' + plural('failure', failureCount);
+
+        if (pendingCount) {
+          specCounts += ', ' + pendingCount + ' pending ' + plural('spec', pendingCount);
+        }
+
+        print(specCounts);
+      } else {
+        print('No specs found');
+      }
+
+      printNewline();
+      var seconds = timer.elapsed() / 1000;
+      print('Finished in ' + seconds + ' ' + plural('second', seconds));
+      printNewline();
+
+      for(i = 0; i < failedSuites.length; i++) {
+        suiteFailureDetails(failedSuites[i]);
+      }
+
+      onComplete(failureCount === 0);
+    };
+
+    this.specDone = function(result) {
+      specCount++;
+
+      if (result.status == 'pending') {
+        pendingCount++;
+        print(colored('yellow', '*'));
+        return;
+      }
+
+      if (result.status == 'passed') {
+        print(colored('green', '.'));
+        return;
+      }
+
+      if (result.status == 'failed') {
+        failureCount++;
+        failedSpecs.push(result);
+        print(colored('red', 'F'));
+      }
+    };
+
+    this.suiteDone = function(result) {
+      if (result.failedExpectations && result.failedExpectations.length > 0) {
+        failureCount++;
+        failedSuites.push(result);
+      }
+    };
+
+    return this;
+
+    function printNewline() {
+      print('\n');
+    }
+
+    function colored(color, str) {
+      return showColors ? (ansi[color] + str + ansi.none) : str;
+    }
+
+    function plural(str, count) {
+      return count == 1 ? str : str + 's';
+    }
+
+    function repeat(thing, times) {
+      var arr = [];
+      for (var i = 0; i < times; i++) {
+        arr.push(thing);
+      }
+      return arr;
+    }
+
+    function indent(str, spaces) {
+      var lines = (str || '').split('\n');
+      var newArr = [];
+      for (var i = 0; i < lines.length; i++) {
+        newArr.push(repeat(' ', spaces).join('') + lines[i]);
+      }
+      return newArr.join('\n');
+    }
+
+    function specFailureDetails(result) {
+      printNewline();
+      print(result.fullName);
+
+      for (var i = 0; i < result.failedExpectations.length; i++) {
+        var failedExpectation = result.failedExpectations[i];
+        printNewline();
+        print(indent(failedExpectation.message, 2));
+        print(indent(failedExpectation.stack, 2));
+      }
+
+      printNewline();
+    }
+
+    function suiteFailureDetails(result) {
+      for (var i = 0; i < result.failedExpectations.length; i++) {
+        printNewline();
+        print(colored('red', 'An error was thrown in an afterAll'));
+        printNewline();
+        print(colored('red', 'AfterAll ' + result.failedExpectations[i].message));
+
+      }
+      printNewline();
+    }
+  }
+
+  return ConsoleReporter;
+};

jasmine/matchers/custom.js

+var customMatchers = {
+	toBeDatasetValues : function(util, customEqualityTesters) {
+		return {
+			compare : function(actual, expected, tol) {
+				if (!tol) {
+					tol = 0;
+				}
+				if (actual.getRowCount() != expected.getRowCount()
+						|| actual.getColumnCount() != expected.getColumnCount()) {
+					return {
+						message : 'Dimensions differ'
+					};
+				}
+				for (var i = 0; i < actual.getRowCount(); i++) {
+					for (var j = 0; j < expected.getColumnCount(); j++) {
+						if (Math.abs(actual.getValue(i, j)
+								- expected.getValue(i, j)) > tol) {
+							return {
+								message : 'Values differ at ' + i + ',' + j
+										+ ' ' + actual.getValue(i, j) + ' != '
+										+ expected.getValue(i, j)
+							};
+						}
+					}
+				}
+				return {
+					pass : true
+				};
+			}
+		}
+	}
+};
+
+beforeEach(function() {
+	jasmine.addMatchers(customMatchers);
+});
\ No newline at end of file

jasmine/spec/adjust_tool_test.js

+describe("adjust_tool_test", function() {
+
+	it("log", function() {
+		var heatmap = new morpheus.HeatMap({
+			dataset : new morpheus.Dataset({
+				array : [ [ 1, 2 ], [ 3, 4 ] ],
+				rows : 2,
+				columns : 2
+			})
+		});
+
+		new morpheus.AdjustDataTool().execute({
+			controller : heatmap,
+			project : heatmap.getProject(),
+			input : {
+				log_2 : true
+			}
+		});
+		expect(heatmap.getProject().getFullDataset()).toBeDatasetValues(
+				new morpheus.Dataset({
+					array : [ [ 0, 1 ], [ 1.584963, 2 ] ],
+					rows : 2,
+					columns : 2
+				}), 0.00001);
+
+		new morpheus.AdjustDataTool().execute({
+			controller : heatmap,
+			project : heatmap.getProject(),
+			input : {
+				inverse_log_2 : true
+			}
+		});
+
+		expect(heatmap.getProject().getFullDataset()).toBeDatasetValues(
+				new morpheus.Dataset({
+					array : [ [ 1, 2 ], [ 3, 4 ] ],
+					rows : 2,
+					columns : 2
+				}), 0.00001);
+
+	});
+	it('z-score', function() {
+		// v = (v-m)/u
+		var heatmap = new morpheus.HeatMap({
+			dataset : new morpheus.Dataset({
+				array : [ [ 1, 2, 10 ], [ 3, 4, 15 ] ],
+				rows : 2,
+				columns : 3
+			})
+		});
+
+		// var r_sd = [ 4.932883, 6.658328 ];
+		// var r_mean = [ 4.333333, 7.333333 ];
+		new morpheus.AdjustDataTool().execute({
+			controller : heatmap,
+			project : heatmap.getProject(),
+			input : {
+				'z-score' : true
+			}
+		});
+		expect(heatmap.getProject().getFullDataset()).toBeDatasetValues(
+				new morpheus.Dataset({
+					array : [ [ -0.6757374, -0.4730162, 1.1487535 ],
+							[ -0.6508140, -0.5006262, 1.1514402 ] ],
+					rows : 2,
+					columns : 3
+				}), 0.00001);
+	});
+
+	it('robust z-score', function() {
+		// v = (v-m)/u
+		var heatmap = new morpheus.HeatMap({
+			dataset : new morpheus.Dataset({
+				array : [ [ 1, 2, 10 ], [ 3, 4, 15 ] ],
+				rows : 2,
+				columns : 3
+			})
+		});
+
+		// var r_mad = [ 1.4826, 1.4826 ];
+		// var r_median = [ 2, 4];
+		new morpheus.AdjustDataTool().execute({
+			controller : heatmap,
+			project : heatmap.getProject(),
+			input : {
+				'robust_z-score' : true
+			}
+		});
+		expect(heatmap.getProject().getFullDataset()).toBeDatasetValues(
+				new morpheus.Dataset({
+					array : [ [ -0.6744908, 0.0000000, 5.3959261 ],
+							[ -0.6744908, 0.0000000, 7.4193984 ] ],
+					rows : 2,
+					columns : 3
+				}), 0.00001);
+	});
+
+});

jasmine/spec/ranking_test.js

+describe("ranking_test", function() {
+	it("R ties", function() {
+		var x2 = [ 3, 1, 4, 1, 5, 9, 2, 6, 5, 3, 5 ];
+		expect(morpheus.Ranking(x2)).toEqual(
+				[ 4.5, 1.5, 6.0, 1.5, 8.0, 11.0, 3.0, 10.0, 8.0, 4.5, 8.0 ]);
+
+	});
+	it("R no ties", function() {
+		expect(morpheus.Ranking([ 3, 1, 4, 15, 92 ]))
+				.toEqual([ 2, 1, 3, 4, 5 ]);
+
+	});
+});

js/FileSaver.min.js

+/*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */
+var saveAs=saveAs||function(view){"use strict";if(typeof navigator!=="undefined"&&/MSIE [1-9]\./.test(navigator.userAgent)){return}var doc=view.document,get_URL=function(){return view.URL||view.webkitURL||view},save_link=doc.createElementNS("http://www.w3.org/1999/xhtml","a"),can_use_save_link="download"in save_link,click=function(node){var event=new MouseEvent("click");node.dispatchEvent(event)},is_safari=/Version\/[\d\.]+.*Safari/.test(navigator.userAgent),webkit_req_fs=view.webkitRequestFileSystem,req_fs=view.requestFileSystem||webkit_req_fs||view.mozRequestFileSystem,throw_outside=function(ex){(view.setImmediate||view.setTimeout)(function(){throw ex},0)},force_saveable_type="application/octet-stream",fs_min_size=0,arbitrary_revoke_timeout=500,revoke=function(file){var revoker=function(){if(typeof 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js/clipboard.min.js

+/*!
+ * clipboard.js v1.5.7
+ * https://zenorocha.github.io/clipboard.js
+ *
+ * Licensed MIT © Zeno Rocha
+ */
+!function(t){if("object"==typeof exports&&"undefined"!=typeof module)module.exports=t();else if("function"==typeof define&&define.amd)define([],t);else{var e;e="undefined"!=typeof window?window:"undefined"!=typeof global?global:"undefined"!=typeof self?self:this,e.Clipboard=t()}}(function(){var t,e,n;return function t(e,n,r){function o(a,c){if(!n[a]){if(!e[a]){var s="function"==typeof require&&require;if(!c&&s)return s(a,!0);if(i)return i(a,!0);var u=new Error("Cannot find module '"+a+"'");throw u.code="MODULE_NOT_FOUND",u}var l=n[a]={exports:{}};e[a][0].call(l.exports,function(t){var n=e[a][1][t];return o(n?n:t)},l,l.exports,t,e,n,r)}return n[a].exports}for(var i="function"==typeof require&&require,a=0;a<r.length;a++)o(r[a]);return o}({1:[function(t,e,n){var r=t("matches-selector");e.exports=function(t,e,n){for(var o=n?t:t.parentNode;o&&o!==document;){if(r(o,e))return o;o=o.parentNode}}},{"matches-selector":5}],2:[function(t,e,n){function r(t,e,n,r,i){var 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\ No newline at end of file