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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="author" content="Zuguang Gu (z.gu@dkfz.de)" />
<meta name="date" content="2020-06-10" />
<title>Generate Global Options</title>
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* Includes: core.js, widget.js, mouse.js, position.js, draggable.js, droppable.js, resizable.js, selectable.js, sortable.js, accordion.js, autocomplete.js, button.js, dialog.js, menu.js, progressbar.js, selectmenu.js, slider.js, spinner.js, tabs.js, tooltip.js, effect.js, effect-blind.js, effect-bounce.js, effect-clip.js, effect-drop.js, effect-explode.js, effect-fade.js, effect-fold.js, effect-highlight.js, effect-puff.js, effect-pulsate.js, effect-scale.js, effect-shake.js, effect-size.js, effect-slide.js, effect-transfer.js
* Copyright jQuery Foundation and other contributors; Licensed MIT */
(function(e){"function"==typeof define&&define.amd?define(["jquery"],e):e(jQuery)})(function(e){function t(t,s){var n,a,o,r=t.nodeName.toLowerCase();return"area"===r?(n=t.parentNode,a=n.name,t.href&&a&&"map"===n.nodeName.toLowerCase()?(o=e("img[usemap='#"+a+"']")[0],!!o&&i(o)):!1):(/^(input|select|textarea|button|object)$/.test(r)?!t.disabled:"a"===r?t.href||s:s)&&i(t)}function i(t){return e.expr.filters.visible(t)&&!e(t).parents().addBack().filter(function(){return"hidden"===e.css(this,"visibility")}).length}function s(e){return function(){var t=this.element.val();e.apply(this,arguments),this._refresh(),t!==this.element.val()&&this._trigger("change")}}e.ui=e.ui||{},e.extend(e.ui,{version:"1.11.4",keyCode:{BACKSPACE:8,COMMA:188,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,LEFT:37,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SPACE:32,TAB:9,UP:38}}),e.fn.extend({scrollParent:function(t){var i=this.css("position"),s="absolute"===i,n=t?/(auto|scroll|hidden)/:/(auto|scroll)/,a=this.parents().filter(function(){var t=e(this);return s&&"static"===t.css("position")?!1:n.test(t.css("overflow")+t.css("overflow-y")+t.css("overflow-x"))}).eq(0);return"fixed"!==i&&a.length?a:e(this[0].ownerDocument||document)},uniqueId:function(){var e=0;return function(){return this.each(function(){this.id||(this.id="ui-id-"+ ++e)})}}(),removeUniqueId:function(){return this.each(function(){/^ui-id-\d+$/.test(this.id)&&e(this).removeAttr("id")})}}),e.extend(e.expr[":"],{data:e.expr.createPseudo?e.expr.createPseudo(function(t){return function(i){return!!e.data(i,t)}}):function(t,i,s){return!!e.data(t,s[3])},focusable:function(i){return t(i,!isNaN(e.attr(i,"tabindex")))},tabbable:function(i){var s=e.attr(i,"tabindex"),n=isNaN(s);return(n||s>=0)&&t(i,!n)}}),e("<a>").outerWidth(1).jquery||e.each(["Width","Height"],function(t,i){function s(t,i,s,a){return e.each(n,function(){i-=parseFloat(e.css(t,"padding"+this))||0,s&&(i-=parseFloat(e.css(t,"border"+this+"Width"))||0),a&&(i-=parseFloat(e.css(t,"margin"+this))||0)}),i}var n="Width"===i?["Left","Right"]:["Top","Bottom"],a=i.toLowerCase(),o={innerWidth:e.fn.innerWidth,innerHeight:e.fn.innerHeight,outerWidth:e.fn.outerWidth,outerHeight:e.fn.outerHeight};e.fn["inner"+i]=function(t){return void 0===t?o["inner"+i].call(this):this.each(function(){e(this).css(a,s(this,t)+"px")})},e.fn["outer"+i]=function(t,n){return"number"!=typeof t?o["outer"+i].call(this,t):this.each(function(){e(this).css(a,s(this,t,!0,n)+"px")})}}),e.fn.addBack||(e.fn.addBack=function(e){return this.add(null==e?this.prevObject:this.prevObject.filter(e))}),e("<a>").data("a-b","a").removeData("a-b").data("a-b")&&(e.fn.removeData=function(t){return function(i){return arguments.length?t.call(this,e.camelCase(i)):t.call(this)}}(e.fn.removeData)),e.ui.ie=!!/msie [\w.]+/.exec(navigator.userAgent.toLowerCase()),e.fn.extend({focus:function(t){return function(i,s){return"number"==typeof i?this.each(function(){var t=this;setTimeout(function(){e(t).focus(),s&&s.call(t)},i)}):t.apply(this,arguments)}}(e.fn.focus),disableSelection:function(){var e="onselectstart"in document.createElement("div")?"selectstart":"mousedown";return function(){return this.bind(e+".ui-disableSelection",function(e){e.preventDefault()})}}(),enableSelection:function(){return this.unbind(".ui-disableSelection")},zIndex:function(t){if(void 0!==t)return this.css("zIndex",t);if(this.length)for(var i,s,n=e(this[0]);n.length&&n[0]!==document;){if(i=n.css("position"),("absolute"===i||"relative"===i||"fixed"===i)&&(s=parseInt(n.css("zIndex"),10),!isNaN(s)&&0!==s))return s;n=n.parent()}return 0}}),e.ui.plugin={add:function(t,i,s){var n,a=e.ui[t].prototype;for(n in s)a.plugins[n]=a.plugins[n]||[],a.plugins[n].push([i,s[n]])},call:function(e,t,i,s){var n,a=e.plugins[t];if(a&&(s||e.element[0].parentNode&&11!==e.element[0].parentNode.nodeType))for(n=0;a.length>n;n++)e.options[a[n][0]]&&a[n][1].apply(e.element,i)}};var n=0,a=Array.prototype.slice;e.cleanData=function(t){return function(i){var s,n,a;for(a=0;null!=(n=i[a]);a++)try{s=e._data(n,"events"),s&&s.remove&&e(n).triggerHandler("remove
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<style type="text/css">
.tocify {
width: 20%;
max-height: 90%;
overflow: auto;
margin-left: 2%;
position: fixed;
border: 1px solid #ccc;
border-radius: 6px;
}
.tocify ul, .tocify li {
list-style: none;
margin: 0;
padding: 0;
border: none;
line-height: 30px;
}
.tocify-header {
text-indent: 10px;
}
.tocify-subheader {
text-indent: 20px;
display: none;
}
.tocify-subheader li {
font-size: 12px;
}
.tocify-subheader .tocify-subheader {
text-indent: 30px;
}
.tocify-subheader .tocify-subheader .tocify-subheader {
text-indent: 40px;
}
.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader {
text-indent: 50px;
}
.tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader .tocify-subheader {
text-indent: 60px;
}
.tocify .tocify-item > a, .tocify .nav-list .nav-header {
margin: 0px;
}
.tocify .tocify-item a, .tocify .list-group-item {
padding: 5px;
}
.tocify .nav-pills > li {
float: none;
}
</style>
<script>/* jquery Tocify - v1.9.1 - 2013-10-22
* http://www.gregfranko.com/jquery.tocify.js/
* Copyright (c) 2013 Greg Franko; Licensed MIT */
// Immediately-Invoked Function Expression (IIFE) [Ben Alman Blog Post](http://benalman.com/news/2010/11/immediately-invoked-function-expression/) that calls another IIFE that contains all of the plugin logic. I used this pattern so that anyone viewing this code would not have to scroll to the bottom of the page to view the local parameters that were passed to the main IIFE.
(function(tocify) {
// ECMAScript 5 Strict Mode: [John Resig Blog Post](http://ejohn.org/blog/ecmascript-5-strict-mode-json-and-more/)
"use strict";
// Calls the second IIFE and locally passes in the global jQuery, window, and document objects
tocify(window.jQuery, window, document);
}
// Locally passes in `jQuery`, the `window` object, the `document` object, and an `undefined` variable. The `jQuery`, `window` and `document` objects are passed in locally, to improve performance, since javascript first searches for a variable match within the local variables set before searching the global variables set. All of the global variables are also passed in locally to be minifier friendly. `undefined` can be passed in locally, because it is not a reserved word in JavaScript.
(function($, window, document, undefined) {
// ECMAScript 5 Strict Mode: [John Resig Blog Post](http://ejohn.org/blog/ecmascript-5-strict-mode-json-and-more/)
"use strict";
var tocClassName = "tocify",
tocClass = "." + tocClassName,
tocFocusClassName = "tocify-focus",
tocHoverClassName = "tocify-hover",
hideTocClassName = "tocify-hide",
hideTocClass = "." + hideTocClassName,
headerClassName = "tocify-header",
headerClass = "." + headerClassName,
subheaderClassName = "tocify-subheader",
subheaderClass = "." + subheaderClassName,
itemClassName = "tocify-item",
itemClass = "." + itemClassName,
extendPageClassName = "tocify-extend-page",
extendPageClass = "." + extendPageClassName;
// Calling the jQueryUI Widget Factory Method
$.widget("toc.tocify", {
//Plugin version
version: "1.9.1",
// These options will be used as defaults
options: {
// **context**: Accepts String: Any jQuery selector
// The container element that holds all of the elements used to generate the table of contents
context: "body",
// **ignoreSelector**: Accepts String: Any jQuery selector
// A selector to any element that would be matched by selectors that you wish to be ignored
ignoreSelector: null,
// **selectors**: Accepts an Array of Strings: Any jQuery selectors
// The element's used to generate the table of contents. The order is very important since it will determine the table of content's nesting structure
selectors: "h1, h2, h3",
// **showAndHide**: Accepts a boolean: true or false
// Used to determine if elements should be shown and hidden
showAndHide: true,
// **showEffect**: Accepts String: "none", "fadeIn", "show", or "slideDown"
// Used to display any of the table of contents nested items
showEffect: "slideDown",
// **showEffectSpeed**: Accepts Number (milliseconds) or String: "slow", "medium", or "fast"
// The time duration of the show animation
showEffectSpeed: "medium",
// **hideEffect**: Accepts String: "none", "fadeOut", "hide", or "slideUp"
// Used to hide any of the table of contents nested items
hideEffect: "slideUp",
// **hideEffectSpeed**: Accepts Number (milliseconds) or String: "slow", "medium", or "fast"
// The time duration of the hide animation
hideEffectSpeed: "medium",
// **smoothScroll**: Accepts a boolean: true or false
// Determines if a jQuery animation should be used to scroll to specific table of contents items on the page
smoothScroll: true,
// **smoothScrollSpeed**: Accepts Number (milliseconds) or String: "slow", "medium", or "fast"
// The time duration of the smoothScroll animation
smoothScrollSpeed: "medium",
// **scrollTo**: Accepts Number (pixels)
// The amount of space between the top of page and the selected table of contents item after the page has been scrolled
scrollTo: 0,
// **showAndHideOnScroll**: Accepts a boolean: true or false
// Determines if table of contents nested items should be shown and hidden while scrolling
showAndHideOnScroll: true,
// **highlightOnScroll**: Accepts a boolean: true or false
// Determines if table of contents nested items should be highlighted (set to a different color) while scrolling
highlightOnScroll: true,
// **highlightOffset**: Accepts a number
// The offset distance in pixels to trigger the next active table of contents item
highlightOffset: 40,
// **theme**: Accepts a string: "bootstrap", "jqueryui", or "none"
// Determines if Twitter Bootstrap, jQueryUI, or Tocify classes should be added to the table of contents
theme: "bootstrap",
// **extendPage**: Accepts a boolean: true or false
// If a user scrolls to the bottom of the page and the page is not tall enough to scroll to the last table of contents item, then the page height is increased
extendPage: true,
// **extendPageOffset**: Accepts a number: pixels
// How close to the bottom of the page a user must scroll before the page is extended
extendPageOffset: 100,
// **history**: Accepts a boolean: true or false
// Adds a hash to the page url to maintain history
history: true,
// **scrollHistory**: Accepts a boolean: true or false
// Adds a hash to the page url, to maintain history, when scrolling to a TOC item
scrollHistory: false,
// **hashGenerator**: How the hash value (the anchor segment of the URL, following the
// # character) will be generated.
//
// "compact" (default) - #CompressesEverythingTogether
// "pretty" - #looks-like-a-nice-url-and-is-easily-readable
// function(text, element){} - Your own hash generation function that accepts the text as an
// argument, and returns the hash value.
hashGenerator: "compact",
// **highlightDefault**: Accepts a boolean: true or false
// Set's the first TOC item as active if no other TOC item is active.
highlightDefault: true
},
// _Create
// -------
// Constructs the plugin. Only called once.
_create: function() {
var self = this;
self.extendPageScroll = true;
// Internal array that keeps track of all TOC items (Helps to recognize if there are duplicate TOC item strings)
self.items = [];
// Generates the HTML for the dynamic table of contents
self._generateToc();
// Adds CSS classes to the newly generated table of contents HTML
self._addCSSClasses();
self.webkit = (function() {
for (var prop in window) {
if (prop) {
if (prop.toLowerCase().indexOf("webkit") !== -1) {
return true;
}
}
}
return false;
}());
// Adds jQuery event handlers to the newly generated table of contents
self._setEventHandlers();
// Binding to the Window load event to make sure the correct scrollTop is calculated
$(window).load(function() {
// Sets the active TOC item
self._setActiveElement(true);
// Once all animations on the page are complete, this callback function will be called
$("html, body").promise().done(function() {
setTimeout(function() {
self.extendPageScroll = false;
}, 0);
});
});
},
// _generateToc
// ------------
// Generates the HTML for the dynamic table of contents
_generateToc: function() {
// _Local variables_
// Stores the plugin context in the self variable
var self = this,
// All of the HTML tags found within the context provided (i.e. body) that match the top level jQuery selector above
firstElem,
// Instantiated variable that will store the top level newly created unordered list DOM element
ul,
ignoreSelector = self.options.ignoreSelector;
// Determine the element to start the toc with
// get all the top level selectors
firstElem = [];
var selectors = this.options.selectors.replace(/ /g, "").split(",");
// find the first set that have at least one non-ignored element
for(var i = 0; i < selectors.length; i++) {
var foundSelectors = $(this.options.context).find(selectors[i]);
for (var s = 0; s < foundSelectors.length; s++) {
if (!$(foundSelectors[s]).is(ignoreSelector)) {
firstElem = foundSelectors;
break;
}
}
if (firstElem.length> 0)
break;
}
if (!firstElem.length) {
self.element.addClass(hideTocClassName);
return;
}
self.element.addClass(tocClassName);
// Loops through each top level selector
firstElem.each(function(index) {
//If the element matches the ignoreSelector then we skip it
if ($(this).is(ignoreSelector)) {
return;
}
// Creates an unordered list HTML element and adds a dynamic ID and standard class name
ul = $("<ul/>", {
"id": headerClassName + index,
"class": headerClassName
}).
// Appends a top level list item HTML element to the previously created HTML header
append(self._nestElements($(this), index));
// Add the created unordered list element to the HTML element calling the plugin
self.element.append(ul);
// Finds all of the HTML tags between the header and subheader elements
$(this).nextUntil(this.nodeName.toLowerCase()).each(function() {
// If there are no nested subheader elemements
if ($(this).find(self.options.selectors).length === 0) {
// Loops through all of the subheader elements
$(this).filter(self.options.selectors).each(function() {
//If the element matches the ignoreSelector then we skip it
if ($(this).is(ignoreSelector)) {
return;
}
self._appendSubheaders.call(this, self, ul);
});
}
// If there are nested subheader elements
else {
// Loops through all of the subheader elements
$(this).find(self.options.selectors).each(function() {
//If the element matches the ignoreSelector then we skip it
if ($(this).is(ignoreSelector)) {
return;
}
self._appendSubheaders.call(this, self, ul);
});
}
});
});
},
_setActiveElement: function(pageload) {
var self = this,
hash = window.location.hash.substring(1),
elem = self.element.find('li[data-unique="' + hash + '"]');
if (hash.length) {
// Removes highlighting from all of the list item's
self.element.find("." + self.focusClass).removeClass(self.focusClass);
// Highlights the current list item that was clicked
elem.addClass(self.focusClass);
// Triggers the click event on the currently focused TOC item
elem.click();
} else {
// Removes highlighting from all of the list item's
self.element.find("." + self.focusClass).removeClass(self.focusClass);
if (!hash.length && pageload && self.options.highlightDefault) {
// Highlights the first TOC item if no other items are highlighted
self.element.find(itemClass).first().addClass(self.focusClass);
}
}
return self;
},
// _nestElements
// -------------
// Helps create the table of contents list by appending nested list items
_nestElements: function(self, index) {
var arr, item, hashValue;
arr = $.grep(this.items, function(item) {
return item === self.text();
});
// If there is already a duplicate TOC item
if (arr.length) {
// Adds the current TOC item text and index (for slight randomization) to the internal array
this.items.push(self.text() + index);
}
// If there not a duplicate TOC item
else {
// Adds the current TOC item text to the internal array
this.items.push(self.text());
}
hashValue = this._generateHashValue(arr, self, index);
// Appends a list item HTML element to the last unordered list HTML element found within the HTML element calling the plugin
item = $("<li/>", {
// Sets a common class name to the list item
"class": itemClassName,
"data-unique": hashValue
});
if (this.options.theme !== "bootstrap3") {
item.append($("<a/>", {
"html": self.html()
}));
} else {
item.html(self.html());
}
// Adds an HTML anchor tag before the currently traversed HTML element
self.before($("<div/>", {
// Sets a name attribute on the anchor tag to the text of the currently traversed HTML element (also making sure that all whitespace is replaced with an underscore)
"name": hashValue,
"data-unique": hashValue
}));
return item;
},
// _generateHashValue
// ------------------
// Generates the hash value that will be used to refer to each item.
_generateHashValue: function(arr, self, index) {
var hashValue = "",
hashGeneratorOption = this.options.hashGenerator;
if (hashGeneratorOption === "pretty") {
// prettify the text
hashValue = self.text().toLowerCase().replace(/\s/g, "-");
// fix double hyphens
while (hashValue.indexOf("--") > -1) {
hashValue = hashValue.replace(/--/g, "-");
}
// fix colon-space instances
while (hashValue.indexOf(":-") > -1) {
hashValue = hashValue.replace(/:-/g, "-");
}
} else if (typeof hashGeneratorOption === "function") {
// call the function
hashValue = hashGeneratorOption(self.text(), self);
} else {
// compact - the default
hashValue = self.text().replace(/\s/g, "");
}
// add the index if we need to
if (arr.length) {
hashValue += "" + index;
}
// return the value
return hashValue;
},
// _appendElements
// ---------------
// Helps create the table of contents list by appending subheader elements
_appendSubheaders: function(self, ul) {
// The current element index
var index = $(this).index(self.options.selectors),
// Finds the previous header DOM element
previousHeader = $(self.options.selectors).eq(index - 1),
currentTagName = +$(this).prop("tagName").charAt(1),
previousTagName = +previousHeader.prop("tagName").charAt(1),
lastSubheader;
// If the current header DOM element is smaller than the previous header DOM element or the first subheader
if (currentTagName < previousTagName) {
// Selects the last unordered list HTML found within the HTML element calling the plugin
self.element.find(subheaderClass + "[data-tag=" + currentTagName + "]").last().append(self._nestElements($(this), index));
}
// If the current header DOM element is the same type of header(eg. h4) as the previous header DOM element
else if (currentTagName === previousTagName) {
ul.find(itemClass).last().after(self._nestElements($(this), index));
} else {
// Selects the last unordered list HTML found within the HTML element calling the plugin
ul.find(itemClass).last().
// Appends an unorderedList HTML element to the dynamic `unorderedList` variable and sets a common class name
after($("<ul/>", {
"class": subheaderClassName,
"data-tag": currentTagName
})).next(subheaderClass).
// Appends a list item HTML element to the last unordered list HTML element found within the HTML element calling the plugin
append(self._nestElements($(this), index));
}
},
// _setEventHandlers
// ----------------
// Adds jQuery event handlers to the newly generated table of contents
_setEventHandlers: function() {
// _Local variables_
// Stores the plugin context in the self variable
var self = this,
// Instantiates a new variable that will be used to hold a specific element's context
$self,
// Instantiates a new variable that will be used to determine the smoothScroll animation time duration
duration;
// Event delegation that looks for any clicks on list item elements inside of the HTML element calling the plugin
this.element.on("click.tocify", "li", function(event) {
if (self.options.history) {
window.location.hash = $(this).attr("data-unique");
}
// Removes highlighting from all of the list item's
self.element.find("." + self.focusClass).removeClass(self.focusClass);
// Highlights the current list item that was clicked
$(this).addClass(self.focusClass);
// If the showAndHide option is true
if (self.options.showAndHide) {
var elem = $('li[data-unique="' + $(this).attr("data-unique") + '"]');
self._triggerShow(elem);
}
self._scrollTo($(this));
});
// Mouseenter and Mouseleave event handlers for the list item's within the HTML element calling the plugin
this.element.find("li").on({
// Mouseenter event handler
"mouseenter.tocify": function() {
// Adds a hover CSS class to the current list item
$(this).addClass(self.hoverClass);
// Makes sure the cursor is set to the pointer icon
$(this).css("cursor", "pointer");
},
// Mouseleave event handler
"mouseleave.tocify": function() {
if (self.options.theme !== "bootstrap") {
// Removes the hover CSS class from the current list item
$(this).removeClass(self.hoverClass);
}
}
});
// only attach handler if needed (expensive in IE)
if (self.options.extendPage || self.options.highlightOnScroll || self.options.scrollHistory || self.options.showAndHideOnScroll) {
// Window scroll event handler
$(window).on("scroll.tocify", function() {
// Once all animations on the page are complete, this callback function will be called
$("html, body").promise().done(function() {
// Local variables
// Stores how far the user has scrolled
var winScrollTop = $(window).scrollTop(),
// Stores the height of the window
winHeight = $(window).height(),
// Stores the height of the document
docHeight = $(document).height(),
scrollHeight = $("body")[0].scrollHeight,
// Instantiates a variable that will be used to hold a selected HTML element
elem,
lastElem,
lastElemOffset,
currentElem;
if (self.options.extendPage) {
// If the user has scrolled to the bottom of the page and the last toc item is not focused
if ((self.webkit && winScrollTop >= scrollHeight - winHeight - self.options.extendPageOffset) || (!self.webkit && winHeight + winScrollTop > docHeight - self.options.extendPageOffset)) {
if (!$(extendPageClass).length) {
lastElem = $('div[data-unique="' + $(itemClass).last().attr("data-unique") + '"]');
if (!lastElem.length) return;
// Gets the top offset of the page header that is linked to the last toc item
lastElemOffset = lastElem.offset().top;
// Appends a div to the bottom of the page and sets the height to the difference of the window scrollTop and the last element's position top offset
$(self.options.context).append($("<div/>", {
"class": extendPageClassName,
"height": Math.abs(lastElemOffset - winScrollTop) + "px",
"data-unique": extendPageClassName
}));
if (self.extendPageScroll) {
currentElem = self.element.find('li.' + self.focusClass);
self._scrollTo($('div[data-unique="' + currentElem.attr("data-unique") + '"]'));
}
}
}
}
// The zero timeout ensures the following code is run after the scroll events
setTimeout(function() {
// _Local variables_
// Stores the distance to the closest anchor
var closestAnchorDistance = null,
// Stores the index of the closest anchor
closestAnchorIdx = null,
// Keeps a reference to all anchors
anchors = $(self.options.context).find("div[data-unique]"),
anchorText;
// Determines the index of the closest anchor
anchors.each(function(idx) {
var distance = Math.abs(($(this).next().length ? $(this).next() : $(this)).offset().top - winScrollTop - self.options.highlightOffset);
if (closestAnchorDistance == null || distance < closestAnchorDistance) {
closestAnchorDistance = distance;
closestAnchorIdx = idx;
} else {
return false;
}
});
anchorText = $(anchors[closestAnchorIdx]).attr("data-unique");
// Stores the list item HTML element that corresponds to the currently traversed anchor tag
elem = $('li[data-unique="' + anchorText + '"]');
// If the `highlightOnScroll` option is true and a next element is found
if (self.options.highlightOnScroll && elem.length) {
// Removes highlighting from all of the list item's
self.element.find("." + self.focusClass).removeClass(self.focusClass);
// Highlights the corresponding list item
elem.addClass(self.focusClass);
}
if (self.options.scrollHistory) {
if (window.location.hash !== "#" + anchorText) {
window.location.replace("#" + anchorText);
}
}
// If the `showAndHideOnScroll` option is true
if (self.options.showAndHideOnScroll && self.options.showAndHide) {
self._triggerShow(elem, true);
}
}, 0);
});
});
}
},
// Show
// ----
// Opens the current sub-header
show: function(elem, scroll) {
// Stores the plugin context in the `self` variable
var self = this,
element = elem;
// If the sub-header is not already visible
if (!elem.is(":visible")) {
// If the current element does not have any nested subheaders, is not a header, and its parent is not visible
if (!elem.find(subheaderClass).length && !elem.parent().is(headerClass) && !elem.parent().is(":visible")) {
// Sets the current element to all of the subheaders within the current header
elem = elem.parents(subheaderClass).add(elem);
}
// If the current element does not have any nested subheaders and is not a header
else if (!elem.children(subheaderClass).length && !elem.parent().is(headerClass)) {
// Sets the current element to the closest subheader
elem = elem.closest(subheaderClass);
}
//Determines what jQuery effect to use
switch (self.options.showEffect) {
//Uses `no effect`
case "none":
elem.show();
break;
//Uses the jQuery `show` special effect
case "show":
elem.show(self.options.showEffectSpeed);
break;
//Uses the jQuery `slideDown` special effect
case "slideDown":
elem.slideDown(self.options.showEffectSpeed);
break;
//Uses the jQuery `fadeIn` special effect
case "fadeIn":
elem.fadeIn(self.options.showEffectSpeed);
break;
//If none of the above options were passed, then a `jQueryUI show effect` is expected
default:
elem.show();
break;
}
}
// If the current subheader parent element is a header
if (elem.parent().is(headerClass)) {
// Hides all non-active sub-headers
self.hide($(subheaderClass).not(elem));
}
// If the current subheader parent element is not a header
else {
// Hides all non-active sub-headers
self.hide($(subheaderClass).not(elem.closest(headerClass).find(subheaderClass).not(elem.siblings())));
}
// Maintains chainablity
return self;
},
// Hide
// ----
// Closes the current sub-header
hide: function(elem) {
// Stores the plugin context in the `self` variable
var self = this;
//Determines what jQuery effect to use
switch (self.options.hideEffect) {
// Uses `no effect`
case "none":
elem.hide();
break;
// Uses the jQuery `hide` special effect
case "hide":
elem.hide(self.options.hideEffectSpeed);
break;
// Uses the jQuery `slideUp` special effect
case "slideUp":
elem.slideUp(self.options.hideEffectSpeed);
break;
// Uses the jQuery `fadeOut` special effect
case "fadeOut":
elem.fadeOut(self.options.hideEffectSpeed);
break;
// If none of the above options were passed, then a `jqueryUI hide effect` is expected
default:
elem.hide();
break;
}
// Maintains chainablity
return self;
},
// _triggerShow
// ------------
// Determines what elements get shown on scroll and click
_triggerShow: function(elem, scroll) {
var self = this;
// If the current element's parent is a header element or the next element is a nested subheader element
if (elem.parent().is(headerClass) || elem.next().is(subheaderClass)) {
// Shows the next sub-header element
self.show(elem.next(subheaderClass), scroll);
}
// If the current element's parent is a subheader element
else if (elem.parent().is(subheaderClass)) {
// Shows the parent sub-header element
self.show(elem.parent(), scroll);
}
// Maintains chainability
return self;
},
// _addCSSClasses
// --------------
// Adds CSS classes to the newly generated table of contents HTML
_addCSSClasses: function() {
// If the user wants a jqueryUI theme
if (this.options.theme === "jqueryui") {
this.focusClass = "ui-state-default";
this.hoverClass = "ui-state-hover";
//Adds the default styling to the dropdown list
this.element.addClass("ui-widget").find(".toc-title").addClass("ui-widget-header").end().find("li").addClass("ui-widget-content");
}
// If the user wants a twitterBootstrap theme
else if (this.options.theme === "bootstrap") {
this.element.find(headerClass + "," + subheaderClass).addClass("nav nav-list");
this.focusClass = "active";
}
// If the user wants a twitterBootstrap theme
else if (this.options.theme === "bootstrap3") {
this.element.find(headerClass + "," + subheaderClass).addClass("list-group");
this.element.find(itemClass).addClass("list-group-item");
this.focusClass = "active";
}
// If a user does not want a prebuilt theme
else {
// Adds more neutral classes (instead of jqueryui)
this.focusClass = tocFocusClassName;
this.hoverClass = tocHoverClassName;
}
//Maintains chainability
return this;
},
// setOption
// ---------
// Sets a single Tocify option after the plugin is invoked
setOption: function() {
// Calls the jQueryUI Widget Factory setOption method
$.Widget.prototype._setOption.apply(this, arguments);
},
// setOptions
// ----------
// Sets a single or multiple Tocify options after the plugin is invoked
setOptions: function() {
// Calls the jQueryUI Widget Factory setOptions method
$.Widget.prototype._setOptions.apply(this, arguments);
},
// _scrollTo
// ---------
// Scrolls to a specific element
_scrollTo: function(elem) {
var self = this,
duration = self.options.smoothScroll || 0,
scrollTo = self.options.scrollTo,
currentDiv = $('div[data-unique="' + elem.attr("data-unique") + '"]');
if (!currentDiv.length) {
return self;
}
// Once all animations on the page are complete, this callback function will be called
$("html, body").promise().done(function() {
// Animates the html and body element scrolltops
$("html, body").animate({
// Sets the jQuery `scrollTop` to the top offset of the HTML div tag that matches the current list item's `data-unique` tag
"scrollTop": currentDiv.offset().top - ($.isFunction(scrollTo) ? scrollTo.call() : scrollTo) + "px"
}, {
// Sets the smoothScroll animation time duration to the smoothScrollSpeed option
"duration": duration
});
});
// Maintains chainability
return self;
}
});
})); //end of plugin
</script>
<script>
/**
* jQuery Plugin: Sticky Tabs
*
* @author Aidan Lister <aidan@php.net>
* adapted by Ruben Arslan to activate parent tabs too
* http://www.aidanlister.com/2014/03/persisting-the-tab-state-in-bootstrap/
*/
(function($) {
"use strict";
$.fn.rmarkdownStickyTabs = function() {
var context = this;
// Show the tab corresponding with the hash in the URL, or the first tab
var showStuffFromHash = function() {
var hash = window.location.hash;
var selector = hash ? 'a[href="' + hash + '"]' : 'li.active > a';
var $selector = $(selector, context);
if($selector.data('toggle') === "tab") {
$selector.tab('show');
// walk up the ancestors of this element, show any hidden tabs
$selector.parents('.section.tabset').each(function(i, elm) {
var link = $('a[href="#' + $(elm).attr('id') + '"]');
if(link.data('toggle') === "tab") {
link.tab("show");
}
});
}
};
// Set the correct tab when the page loads
showStuffFromHash(context);
// Set the correct tab when a user uses their back/forward button
$(window).on('hashchange', function() {
showStuffFromHash(context);
});
// Change the URL when tabs are clicked
$('a', context).on('click', function(e) {
history.pushState(null, null, this.href);
showStuffFromHash(context);
});
return this;
};
}(jQuery));
window.buildTabsets = function(tocID) {
// build a tabset from a section div with the .tabset class
function buildTabset(tabset) {
// check for fade and pills options
var fade = tabset.hasClass("tabset-fade");
var pills = tabset.hasClass("tabset-pills");
var navClass = pills ? "nav-pills" : "nav-tabs";
// determine the heading level of the tabset and tabs
var match = tabset.attr('class').match(/level(\d) /);
if (match === null)
return;
var tabsetLevel = Number(match[1]);
var tabLevel = tabsetLevel + 1;
// find all subheadings immediately below
var tabs = tabset.find("div.section.level" + tabLevel);
if (!tabs.length)
return;
// create tablist and tab-content elements
var tabList = $('<ul class="nav ' + navClass + '" role="tablist"></ul>');
$(tabs[0]).before(tabList);
var tabContent = $('<div class="tab-content"></div>');
$(tabs[0]).before(tabContent);
// build the tabset
var activeTab = 0;
tabs.each(function(i) {
// get the tab div
var tab = $(tabs[i]);
// get the id then sanitize it for use with bootstrap tabs
var id = tab.attr('id');
// see if this is marked as the active tab
if (tab.hasClass('active'))
activeTab = i;
// remove any table of contents entries associated with
// this ID (since we'll be removing the heading element)
$("div#" + tocID + " li a[href='#" + id + "']").parent().remove();
// sanitize the id for use with bootstrap tabs
id = id.replace(/[.\/?&!#<>]/g, '').replace(/\s/g, '_');
tab.attr('id', id);
// get the heading element within it, grab it's text, then remove it
var heading = tab.find('h' + tabLevel + ':first');
var headingText = heading.html();
heading.remove();
// build and append the tab list item
var a = $('<a role="tab" data-toggle="tab">' + headingText + '</a>');
a.attr('href', '#' + id);
a.attr('aria-controls', id);
var li = $('<li role="presentation"></li>');
li.append(a);
tabList.append(li);
// set it's attributes
tab.attr('role', 'tabpanel');
tab.addClass('tab-pane');
tab.addClass('tabbed-pane');
if (fade)
tab.addClass('fade');
// move it into the tab content div
tab.detach().appendTo(tabContent);
});
// set active tab
$(tabList.children('li')[activeTab]).addClass('active');
var active = $(tabContent.children('div.section')[activeTab]);
active.addClass('active');
if (fade)
active.addClass('in');
if (tabset.hasClass("tabset-sticky"))
tabset.rmarkdownStickyTabs();
}
// convert section divs with the .tabset class to tabsets
var tabsets = $("div.section.tabset");
tabsets.each(function(i) {
buildTabset($(tabsets[i]));
});
};
</script>
<style type="text/css">.hljs-literal {
color: #990073;
}
.hljs-number {
color: #099;
}
.hljs-comment {
color: #998;
font-style: italic;
}
.hljs-keyword {
color: #900;
font-weight: bold;
}
.hljs-string {
color: #d14;
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<h1 class="title toc-ignore">Generate Global Options</h1>
<h4 class="author">Zuguang Gu (<a href="mailto:z.gu@dkfz.de" class="email">z.gu@dkfz.de</a>)</h4>
<h4 class="date">2020-06-10</h4>
</div>
<hr />
<p>Global option function such as <code>options()</code> and <code>par()</code> provides a way to control global settings. Here the <strong>GlobalOptions</strong> package provides a more general and controlable way to generate such functions, which can:</p>
<ol style="list-style-type: decimal">
<li>validate the values (e.g. class, length and self-defined validations);</li>
<li>set read-only options;</li>
<li>set invisible options;</li>
<li>set private options which are only accessable in a certain namespace;</li>
<li>support local options and global option;</li>
<li>print options with explanations.</li>
</ol>
<div id="general-usage" class="section level2">
<h2>General usage</h2>
<p>The most simple use is to generate an option function with default values by callling <code>setGlobalOptions()</code> or its short versoin <code>set_opt()</code>:</p>
<pre class="r"><code>library(GlobalOptions)
opt = set_opt(
a = 1,
b = &quot;text&quot;
)</code></pre>
<p>The returned value <code>opt</code> is an option function which can be used to get or set options. Options in <code>opt</code> can be accessed either by specifying as arguments or by using the <code>$</code> operator.</p>
<pre class="r"><code>opt()</code></pre>
<pre><code>$a
[1] 1
$b
[1] &quot;text&quot;</code></pre>
<pre class="r"><code>opt(&quot;a&quot;)</code></pre>
<pre><code>[1] 1</code></pre>
<pre class="r"><code>opt$a</code></pre>
<pre><code>[1] 1</code></pre>
<pre class="r"><code>op = opt()
op</code></pre>
<pre><code>$a
[1] 1
$b
[1] &quot;text&quot;</code></pre>
<pre class="r"><code>opt(a = 2, b = &quot;new text&quot;)
opt()</code></pre>
<pre><code>$a
[1] 2
$b
[1] &quot;new text&quot;</code></pre>
<pre class="r"><code>opt$b = &quot;&quot;
opt()</code></pre>
<pre><code>$a
[1] 2
$b
[1] &quot;&quot;</code></pre>
<pre class="r"><code>opt(op)
opt()</code></pre>
<pre><code>$a
[1] 1
$b
[1] &quot;text&quot;</code></pre>
<p><code>opt</code> generated by <code>set_opt()</code> contains an argument <code>RESET</code> which is used to reset the options to the default:</p>
<pre class="r"><code>opt(a = 2, b = &quot;new text&quot;)
opt(RESET = TRUE)
opt()</code></pre>
<pre><code>$a
[1] 1
$b
[1] &quot;text&quot;</code></pre>
<p>Simply printing <code>opt</code> gives a summary of all options.</p>
<pre class="r"><code>opt</code></pre>
<pre><code> Option Value
------:-------
a 1
b text </code></pre>
</div>
<div id="advanced-usage" class="section level2">
<h2>Advanced usage</h2>
<p>If option values are set as lists, more configurations can be customized.</p>
<div id="simple-validation" class="section level3">
<h3>Simple validation</h3>
<p>There are two basic fields that are used to check the input option values:</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
.length = c(1, 3),
.class = &quot;numeric&quot;)
)</code></pre>
<p>In above code, <code>.value</code> is the default value for the option <code>a</code>. The length of the value is controlled by <code>.length</code> and the length should be either 1 or 3. The class of the value should be <code>numeric</code>. If the input value does not fit these criterions, there will be an error. The value of <code>.length</code> or <code>.class</code> is a vector and the checking will be passed if one of the value fits user’s input.</p>
<pre class="r"><code>opt(a = 1:2) # there will be error because the length is 2</code></pre>
<pre><code>Error: Length of &#39;a&#39; should be one of 1, 3.</code></pre>
<pre class="r"><code>opt(a = &quot;text&quot;) # there will be error because the input is character</code></pre>
<pre><code>Error: Class of &#39;a&#39; should be &#39;numeric&#39;.</code></pre>
</div>
<div id="read-only-options" class="section level3">
<h3>Read-only options</h3>
<p>The value can be set as read-only by <code>.read.only</code> field and modifying such option will cause an error.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
.read.only = TRUE)
)
opt(a = 2) # there will be error because a is read-only</code></pre>
<pre><code>Error: &#39;a&#39; is a read-only option.</code></pre>
<p>There is also a pre-defined argument <code>READ.ONLY</code> in <code>opt()</code> which controls whether to return only the read-only options or not.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
.read.only = TRUE),
b = 2
)
opt(READ.ONLY = TRUE)</code></pre>
<pre><code>$a
[1] 1</code></pre>
<pre class="r"><code>opt(READ.ONLY = FALSE)</code></pre>
<pre><code>$b
[1] 2</code></pre>
<pre class="r"><code>opt(READ.ONLY = NULL) # default, to return both</code></pre>
<pre><code>$a
[1] 1
$b
[1] 2</code></pre>
</div>
<div id="user-defined-validation" class="section level3">
<h3>User-defined validation</h3>
<p>More customized validation of the option values can be controlled by <code>.validate</code> field. The value of <code>.validate</code> should be a function. The input of the validation function is the input option value and the function should only return a logical value.</p>
<p><code>a</code> should only between 0 and 10 in following example.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
.validate = function(x) x &gt; 0 &amp;&amp; x &lt; 10
)
)
opt(a = 20) # This will cause an error</code></pre>
<pre><code>Error: a didn&#39;t pass the validation. Your option is invalid.</code></pre>
<p><code>.failed_msg</code> is used to configure the error message once validation is failed.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
.validate = function(x) x &gt; 0 &amp;&amp; x &lt; 10,
.failed_msg = &quot;&#39;a&#39; should be in (0, 10).&quot;
)
)
opt(a = 20) # This will cause an error</code></pre>
<pre><code>Error: a didn&#39;t pass the validation. &#39;a&#39; should be in (0, 10).</code></pre>
</div>
<div id="filter-the-option-values" class="section level3">
<h3>Filter the option values</h3>
<p>Filtering on the option values can be controlled by <code>.filter</code> field. This is useful when the input option value is not valid but it is not necessary to throw errors. More proper way is to modify the value silently. For example, there is an option to control whether to print messages or not and it should be set to <code>TRUE</code> or <code>FALSE</code>. However, users may set some other type of values such as <code>NULL</code> or <code>NA</code>. In this case, non-<code>TRUE</code> values can be converted to logical values by <code>.filter</code>. Similar as <code>.validate</code>, the input value for filter function is the input option value, and it should return a filtered option value.</p>
<pre class="r"><code>opt = set_opt(
verbose =
list(.value = TRUE,
.filter = function(x) {
if(is.null(x)) {
return(FALSE)
} else if(is.na(x)) {
return(FALSE)
} else {
return(x)
}
})
)
opt(verbose = FALSE); opt(&quot;verbose&quot;)</code></pre>
<pre><code>[1] FALSE</code></pre>
<pre class="r"><code>opt(verbose = NA); opt(&quot;verbose&quot;)</code></pre>
<pre><code>[1] FALSE</code></pre>
<pre class="r"><code>opt(verbose = NULL); opt(&quot;verbose&quot;)</code></pre>
<pre><code>[1] FALSE</code></pre>
<p>Another example is when there is an option which controls four margin values of a plot, the length of the value can either be 1, 2, or 4. With <code>.filter</code>, length can be normaliezd to 4 consistently.</p>
<pre class="r"><code>opt = set_opt(
margin =
list(.value = c(1, 1, 1, 1),
.length = c(1, 2, 4),
.filter = function(x) {
if(length(x) == 1) {
return(rep(x, 4))
} else if(length(x) == 2) {
return(rep(x, 2))
} else {
return(x)
}
})
)
opt(margin = 2); opt(&quot;margin&quot;)</code></pre>
<pre><code>[1] 2 2 2 2</code></pre>
<pre class="r"><code>opt(margin = c(2, 4)); opt(&quot;margin&quot;)</code></pre>
<pre><code>[1] 2 4 2 4</code></pre>
</div>
<div id="dynamic-querying-the-option-value" class="section level3">
<h3>Dynamic querying the option value</h3>
<p>The input option value can be set dynamicly by setting it as a function. When the option value is set as a function and class of the option is non-function, it will be executed when querying the option. In the following example, the <code>prefix</code> option corresponds to the prefix of log messages. The returned option value is the string after the execution of the input function.</p>
<pre class="r"><code>opt = set_opt(
prefix = &quot;&quot;
)
opt(prefix = function() paste(&quot;[&quot;, Sys.time(), &quot;] &quot;, sep = &quot; &quot;))
opt(&quot;prefix&quot;) # or opt$prefix</code></pre>
<pre><code>[1] &quot;[ 2020-06-10 14:34:04 ] &quot;</code></pre>
<pre class="r"><code>Sys.sleep(2)
opt(&quot;prefix&quot;)</code></pre>
<pre><code>[1] &quot;[ 2020-06-10 14:34:06 ] &quot;</code></pre>
<p>If the value of the option is a real function and users don’t want to execute it, just set <code>.class</code> to contain <code>function</code>, then the function will be treated as a simple value.</p>
<pre class="r"><code>opt = set_opt(
test_fun = list(.value = function(x1, x2) t.test(x1, x2)$p.value,
.class = &quot;function&quot;)
)
opt(test_fun = function(x1, x2) cor.test(x1, x2)$p.value)
opt(&quot;test_fun&quot;) # or opt$test_fun</code></pre>
<pre><code>function(x1, x2) cor.test(x1, x2)$p.value</code></pre>
</div>
<div id="interaction-between-options" class="section level3">
<h3>Interaction between options</h3>
<p>The self-defined function (i.e. value function, validation function or filter function) is applied per-option independently. But sometimes we want to set one option based on values of other options. In this case, we need a function which can get other option values. <code>.v()</code> can be used to access other option values defined beforehand. <code>.v(&quot;a&quot;)</code> can also be written as <code>.v(a)</code> or <code>.v$a</code>.</p>
<pre class="r"><code>opt = set_opt(
a = 1,
b = function() 2 * .v$a
)
opt(&quot;b&quot;) # or opt$b</code></pre>
<pre><code>[1] 2</code></pre>
<pre class="r"><code>opt(a = 2)
opt(&quot;b&quot;)</code></pre>
<pre><code>[1] 4</code></pre>
<p>However, you can still overwrite option <code>b</code>:</p>
<pre class="r"><code>opt(a = 2, b = 3) # b was overwriiten and will not be 2*a
opt()</code></pre>
<pre><code>$a
[1] 2
$b
[1] 3</code></pre>
<p><code>.v</code> can also be used in <code>.validate</code> and <code>.filter</code> fields. In the second example, sign of <code>b</code> should be as same as sign of <code>a</code>.</p>
<pre class="r"><code>opt = set_opt(
a = 1,
b = list(.value = 0,
.validate = function(x) {
if(.v$a &gt; 0) x &gt; 0
else x &lt; 0
},
.filter = function(x) {
x + .v$a
},
.failed_msg = &quot;&#39;b&#39; should have same sign as &#39;a&#39;.&quot;)
)
opt(b = 1)
opt(&quot;b&quot;)</code></pre>
<pre><code>[1] 2</code></pre>
<pre class="r"><code>opt(a = 1, b = -1) # this should cause an error</code></pre>
<pre><code>Error: b didn&#39;t pass the validation. &#39;b&#39; should have same sign as &#39;a&#39;.</code></pre>
</div>
<div id="local-options" class="section level3">
<h3>Local options</h3>
<p>The option funtion also has a <code>LOCAL</code> argument which switches local mode and global mode. When <code>LOCAL</code> is set to <code>TRUE</code>, a copy of current options is generated and all queries are applied on the copy version. The local mode is turned off when <code>LOCAL</code> is explicitely specified to <code>FALSE</code>.</p>
<pre class="r"><code>opt = set_opt(
a = 1
)
opt(LOCAL = TRUE)
opt(a = 2)
opt$a</code></pre>
<pre><code>[1] 2</code></pre>
<pre class="r"><code>opt(LOCAL = FALSE)
opt$a</code></pre>
<pre><code>[1] 1</code></pre>
<p>Local mode will be automatically turned off when enrivonment changes. In following example, local mode only works inside <code>f1()</code> and <code>f2()</code> functions and the local copies are independent in <code>f1()</code> and <code>f2()</code>. Note when leaving e.g. <code>f1()</code>, the copy of the option is deleted.</p>
<pre class="r"><code>opt = set_opt(
a = 1
)
f1 = function() {
opt(LOCAL = TRUE)
opt(a = 2)
return(opt$a)
}
f1()</code></pre>
<pre><code>[1] 2</code></pre>
<pre class="r"><code>opt$a</code></pre>
<pre><code>[1] 1</code></pre>
<pre class="r"><code>f2 = function() {
opt(LOCAL = TRUE)
opt(a = 4)
return(opt$a)
}
f2()</code></pre>
<pre><code>[1] 4</code></pre>
<pre class="r"><code>opt$a</code></pre>
<pre><code>[1] 1</code></pre>
<p>If <code>f1()</code> calls <code>f2()</code>, <code>f2()</code> will be in the same local mode as <code>f1()</code>. In other word, all children frames are in a same local mode if the parent frame is in local mode.</p>
<pre class="r"><code>opt = set_opt(
a = 1
)
f1 = function() {
opt(LOCAL = TRUE)
opt(a = 2)
return(f2())
}
f2 = function() {
opt$a
}
f1()</code></pre>
<pre><code>[1] 2</code></pre>
<pre class="r"><code>opt$a</code></pre>
<pre><code>[1] 1</code></pre>
</div>
<div id="synonymous-options" class="section level3">
<h3>Synonymous options</h3>
<p>It can be possible that several weeks later, developers have better names for the options. They want to use the new option names but still do not want to disable the old ones. In this case, <code>.synonymous</code> field can be set to let the new option and old option reference to a same internal option object (which means all other configuration specified for this option is ignored). The change of values of either one will also affect the companions correspondingly.</p>
<pre class="r"><code>opt = set_opt(
old = 1,
new = list(.value = 1,
.synonymous = &quot;old&quot;)
)
opt()</code></pre>
<pre><code>$old
[1] 1
$new
[1] 1</code></pre>
<pre class="r"><code>opt$old = 2
opt()</code></pre>
<pre><code>$old
[1] 2
$new
[1] 2</code></pre>
<pre class="r"><code>opt$new = 3
opt()</code></pre>
<pre><code>$old
[1] 3
$new
[1] 3</code></pre>
</div>
<div id="print-the-object" class="section level3">
<h3>Print the object</h3>
<p>There is a <code>.description</code> field for each option which is only used when printing the summary of options. As shown before, simply entering the option object gives a summary table for all options.</p>
<pre class="r"><code>opt = set_opt(
a = 1,
b = &quot;b&quot;,
c = list(.value = letters[1:4],
.class = &quot;character&quot;,
.description = &quot;26 letters&quot;),
d = list(.value = c(0, 0),
.class = &quot;numeric&quot;,
.validate = function(x) x[1]^2 + x[2]^2 &lt;= 1,
.failed_msg = &quot;The point should be in the unit circle&quot;,
.description = &quot;start points in the unit circle&quot;),
e = list(.value = rnorm,
.class = &quot;function&quot;,
.description = &quot;distribution to generate random numbers and a very long long long long long long long long text&quot;)
)
opt</code></pre>
<pre><code> Option Value
------:------------------------------------------------------------------------
a 1
b b
c a, b, c, d
(26 letters)
d 0, 0
(start points in the unit circle)
e a user-defined function
(distribution to generate random numbers and a very long long long
long long long long long text)</code></pre>
<p>Use <code>dump_opt()</code> to get summary for each option.</p>
<pre class="r"><code>dump_opt(opt, &quot;a&quot;)</code></pre>
<pre><code> Field Value
name a
default_value 1
current_value 1
length no limit
class no limit
validate a user-defined function
failed_msg Your option is invalid.
filter a user-defined function
read.only FALSE
private FALSE
visible TRUE
description &quot;&quot;
__generated_namespace__ R_GlobalEnv</code></pre>
<pre class="r"><code>dump_opt(opt, &quot;d&quot;)</code></pre>
<pre><code> Field Value
name d
default_value 0, 0
current_value 0, 0
length no limit
class numeric
validate a user-defined function
failed_msg The point should be in the unit circle
filter a user-defined function
read.only FALSE
private FALSE
visible TRUE
description start points in the unit circle
__generated_namespace__ R_GlobalEnv</code></pre>
</div>
<div id="add-new-options" class="section level3">
<h3>Add new options</h3>
<p>New options can be added after the option function is created by explicitely specifying <code>ADD = TRUE</code>:</p>
<pre class="r"><code>opt = set_opt(a = 1)
opt(b = 2, ADD = TRUE)
opt</code></pre>
<pre><code> Option Value
------:-------
a 1
b 2 </code></pre>
<p>Note you cannot add new options by using <code>$</code> (or more precisely <code>$&lt;-</code>) operator because <code>$</code> can only access options that have already been created.</p>
<pre class="r"><code>opt$c = 3</code></pre>
<pre><code>Error: No such option: &#39;c&#39;. If you want to add this new option, please use
your_opt_fun(c = ..., ADD = TRUE)</code></pre>
<p>Like using a complex configuration list when creating a new option in <code>set_opt()</code>, here you can also use configuration list with <code>ADD = TRUE</code>.</p>
<pre class="r"><code>opt(c = list(.value = &quot;c&quot;,
.class = &quot;character&quot;),
ADD = TRUE)
opt</code></pre>
<pre><code> Option Value
------:-------
a 1
b 2
c c </code></pre>
<pre class="r"><code>opt$c = 1</code></pre>
<pre><code>Error: Class of &#39;c&#39; should be &#39;character&#39;.</code></pre>
<p>Of course you can put more than one options in <code>opt()</code> when adding them.</p>
</div>
</div>
<div id="features-for-package-development" class="section level2">
<h2>Features for package development</h2>
<p>Two additional fields may be helpful when developing packages. <code>.visible</code> controls whether options are visible to users. The invisible option can only be queried or modified by specifying its option name (just like you can only open the door with the correct unique key). This would be helpful if users want to put some secret options while do not want others to access. Is this case, they can assign names with complex strings like <code>.__MY_PRIVATE_KEY__.</code> as their secret options and afterwards they can access it with this special key.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
.visible = FALSE),
b = 2
)
opt()</code></pre>
<pre><code>$b
[1] 2</code></pre>
<pre class="r"><code>opt$a</code></pre>
<pre><code>[1] 1</code></pre>
<pre class="r"><code>opt$a = 2
opt$a</code></pre>
<pre><code>[1] 2</code></pre>
<pre class="r"><code>opt()</code></pre>
<pre><code>$b
[1] 2</code></pre>
<p>Another field <code>.private</code> controls whether the option is only private to the namespace (e.g. packages). If it is set to <code>TRUE</code>, the option can only be modified in the same namespace (or top environment) where the option function is generated. E.g, if you are writing a package named <strong>foo</strong> and generating an option function <code>foo_opt()</code>, by setting the option with <code>.private</code> to <code>TRUE</code>, the value for such options can only be modified inside <strong>foo</strong> package while it is not permitted outside <strong>foo</strong>. At the same time, private options become read-only options if querying outside <strong>foo</strong> package.</p>
<p>In following example, we manually modify the namespace where <code>set_opt()</code> is called in <code>stats</code> package.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
.private = TRUE)
)
require(stats)
ns = getNamespace(&quot;stats&quot;)
environment(opt)$options$a$`__generated_namespace__` = ns</code></pre>
<p>There will be error if trying to modify <code>a</code> which is private in <code>stats</code> namespace.</p>
<pre class="r"><code>opt$a = 2</code></pre>
<pre><code>Error: &#39;a&#39; is a private option and it can only be modified inside &#39;stats&#39;
namespace while not &#39;R_GlobalEnv&#39;.</code></pre>
<p>But you can still access it.</p>
<pre class="r"><code>opt$a</code></pre>
<pre><code>[1] 1</code></pre>
<p>The option object generated by <code>set_opt()</code> is actually a function. It contains four arguments: <code>...</code>, <code>RESET</code>, <code>READ.ONLY</code>, <code>LOCAL</code>, <code>ADD</code>. If you want to put the option function into a package, remember to document all the four arguments:</p>
<pre class="r"><code>args(opt)</code></pre>
<pre><code>function (..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE,
ADD = FALSE)
NULL</code></pre>
</div>
<div id="misc" class="section level2">
<h2>Misc</h2>
<p>The order of validation when modifying an option value is <code>.read.only</code>, <code>.private</code>, <code>.length</code>, <code>.class</code>, <code>.validate</code>, <code>.filter</code>, <code>.length</code>, <code>.class</code>. Note validation on length and class of the option values will be applied again after filtering.</p>
<p>Global options are stored in private environments. Each time when generating a option function, there will be new environments created. Thus global options will not conflict if they come from different option functions.</p>
<pre class="r"><code>opt1 = set_opt(
a = list(.value = 1)
)
opt2 = set_opt(
a = list(.value = 1)
)
opt1$a = 2
opt1$a</code></pre>
<pre><code>[1] 2</code></pre>
<pre class="r"><code>opt2$a</code></pre>
<pre><code>[1] 1</code></pre>
<p>Note the option values can also be set as a list, so for the list containing configurations, names of the field is started with a dot <code>.</code> to be distinguished from the normal list.</p>
<pre class="r"><code>opt = set_opt(
list = list(a = 1,
b = 2)
)
opt()</code></pre>
<pre><code>$list
$list$a
[1] 1
$list$b
[1] 2</code></pre>
<pre class="r"><code>opt = set_opt(
list = list(.value = list(a = 1, b = 2),
.class = &quot;list&quot;)
)
opt()</code></pre>
<pre><code>$list
$list$a
[1] 1
$list$b
[1] 2</code></pre>
<pre class="r"><code>opt$list = 1 # this will cause an error</code></pre>
<pre><code>Error: Class of &#39;list&#39; should be &#39;list&#39;.</code></pre>
<p>If you made a type of the field names when configurating the options (e.g. forgot to type the leading dot), there will be a warning and the whole configuration list is treated as a normal list for this option.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = 1,
class = &quot;numeric&quot;) # &lt;- here it should be .class
)</code></pre>
<pre><code>Warning: Your definition for &#39;a&#39; is mixed. It should only contain .value,
.class, .length, .validate, .failed_msg, .filter, .read.only, .private,
.visible, .synonymous, .description. Ignore the setting and use the
whole list as the default value.</code></pre>
<pre class="r"><code>opt$a</code></pre>
<pre><code>$.value
[1] 1
$class
[1] &quot;numeric&quot;</code></pre>
<p>The final and the most important thing is the validation by <code>.class</code>, <code>.length</code>, <code>.validate</code>, <code>.filter</code> will not be applied on default values because users who design their option functions should know whether the default values are valid or not.</p>
<pre class="r"><code>opt = set_opt(
a = list(.value = -1,
.validate = function(x) x &gt; 0)
)
opt$a</code></pre>
<pre><code>[1] -1</code></pre>
</div>
<div id="session-info" class="section level2">
<h2>Session info</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GlobalOptions_0.1.2 GetoptLong_1.0.0 knitr_1.28
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 digest_0.6.25 crayon_1.3.4 magrittr_1.5
[5] evaluate_0.14 rlang_0.4.6 stringi_1.4.6 rmarkdown_2.1
[9] rjson_0.2.20 tools_4.0.0 stringr_1.4.0 xfun_0.14
[13] yaml_2.2.1 compiler_4.0.0 htmltools_0.4.0</code></pre>
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