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/** Called automatically by JsDoc Toolkit. */
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function publish(symbolSet) {
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	publish.conf = {  // trailing slash expected for dirs
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		ext:         ".html",
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		outDir:      JSDOC.opt.d || SYS.pwd+"../out/jsdoc/",
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		templatesDir: JSDOC.opt.t || SYS.pwd+"../templates/jsdoc/",
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		symbolsDir:  "symbols/",
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		srcDir:      "symbols/src/"
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	};
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	// is source output is suppressed, just display the links to the source file
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	if (JSDOC.opt.s && defined(Link) && Link.prototype._makeSrcLink) {
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		Link.prototype._makeSrcLink = function(srcFilePath) {
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			return "<"+srcFilePath+">";
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		}
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	}
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	// create the folders and subfolders to hold the output
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	IO.mkPath((publish.conf.outDir+"symbols/src").split("/"));
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	// used to allow Link to check the details of things being linked to
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	Link.symbolSet = symbolSet;
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	// create the required templates
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	try {
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		var classTemplate = new JSDOC.JsPlate(publish.conf.templatesDir+"class.tmpl");
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		var classesTemplate = new JSDOC.JsPlate(publish.conf.templatesDir+"allclasses.tmpl");
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	}
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	catch(e) {
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		print("Couldn't create the required templates: "+e);
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		quit();
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	}
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	// some ustility filters
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	function hasNoParent($) {return ($.memberOf == "")}
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	function isaFile($) {return ($.is("FILE"))}
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	function isaClass($) {return ($.is("CONSTRUCTOR") || $.isNamespace)}
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	// get an array version of the symbolset, useful for filtering
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	var symbols = symbolSet.toArray();
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	// create the hilited source code files
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	var files = JSDOC.opt.srcFiles;
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 	for (var i = 0, l = files.length; i < l; i++) {
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 		var file = files[i];
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 		var srcDir = publish.conf.outDir + "symbols/src/";
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		makeSrcFile(file, srcDir);
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 	}
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 	// get a list of all the classes in the symbolset
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 	var classes = symbols.filter(isaClass).sort(makeSortby("alias"));
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	// create a filemap in which outfiles must be to be named uniquely, ignoring case
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	if (JSDOC.opt.u) {
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		var filemapCounts = {};
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		Link.filemap = {};
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		for (var i = 0, l = classes.length; i < l; i++) {
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			var lcAlias = classes[i].alias.toLowerCase();
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			if (!filemapCounts[lcAlias]) filemapCounts[lcAlias] = 1;
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			else filemapCounts[lcAlias]++;
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			Link.filemap[classes[i].alias] =
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				(filemapCounts[lcAlias] > 1)?
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				lcAlias+"_"+filemapCounts[lcAlias] : lcAlias;
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		}
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	}
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	// create a class index, displayed in the left-hand column of every class page
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	Link.base = "../";
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 	publish.classesIndex = classesTemplate.process(classes); // kept in memory
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	// create each of the class pages
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	for (var i = 0, l = classes.length; i < l; i++) {
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		var symbol = classes[i];
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		symbol.events = symbol.getEvents();   // 1 order matters
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		symbol.methods = symbol.getMethods(); // 2
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		Link.currentSymbol= symbol;
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		var output = "";
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		output = classTemplate.process(symbol);
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		IO.saveFile(publish.conf.outDir+"symbols/", ((JSDOC.opt.u)? Link.filemap[symbol.alias] : symbol.alias) + publish.conf.ext, output);
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	}
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	// regenerate the index with different relative links, used in the index pages
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	Link.base = "";
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	publish.classesIndex = classesTemplate.process(classes);
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	// create the class index page
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	try {
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		var classesindexTemplate = new JSDOC.JsPlate(publish.conf.templatesDir+"index.tmpl");
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	}
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	catch(e) { print(e.message); quit(); }
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	var classesIndex = classesindexTemplate.process(classes);
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	IO.saveFile(publish.conf.outDir, "index"+publish.conf.ext, classesIndex);
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	classesindexTemplate = classesIndex = classes = null;
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	// create the file index page
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	try {
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		var fileindexTemplate = new JSDOC.JsPlate(publish.conf.templatesDir+"allfiles.tmpl");
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	}
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	catch(e) { print(e.message); quit(); }
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	var documentedFiles = symbols.filter(isaFile); // files that have file-level docs
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	var allFiles = []; // not all files have file-level docs, but we need to list every one
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	for (var i = 0; i < files.length; i++) {
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		allFiles.push(new JSDOC.Symbol(files[i], [], "FILE", new JSDOC.DocComment("/** */")));
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	}
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	for (var i = 0; i < documentedFiles.length; i++) {
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		var offset = files.indexOf(documentedFiles[i].alias);
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		allFiles[offset] = documentedFiles[i];
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	}
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	allFiles = allFiles.sort(makeSortby("name"));
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	// output the file index page
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	var filesIndex = fileindexTemplate.process(allFiles);
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	IO.saveFile(publish.conf.outDir, "files"+publish.conf.ext, filesIndex);
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	fileindexTemplate = filesIndex = files = null;
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}
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/** Just the first sentence (up to a full stop). Should not break on dotted variable names. */
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function summarize(desc) {
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	if (typeof desc != "undefined")
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		return desc.match(/([\w\W]+?\.)[^a-z0-9_$]/i)? RegExp.$1 : desc;
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}
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/** Make a symbol sorter by some attribute. */
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function makeSortby(attribute) {
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	return function(a, b) {
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		if (a[attribute] != undefined && b[attribute] != undefined) {
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			a = a[attribute].toLowerCase();
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			b = b[attribute].toLowerCase();
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			if (a < b) return -1;
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			if (a > b) return 1;
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			return 0;
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		}
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	}
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}
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/** Pull in the contents of an external file at the given path. */
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function include(path) {
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	var path = publish.conf.templatesDir+path;
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	return IO.readFile(path);
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}
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/** Turn a raw source file into a code-hilited page in the docs. */
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function makeSrcFile(path, srcDir, name) {
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	if (JSDOC.opt.s) return;
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	if (!name) {
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		name = path.replace(/\.\.?[\\\/]/g, "").replace(/[\\\/]/g, "_");
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		name = name.replace(/\:/g, "_");
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	}
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	var src = {path: path, name:name, charset: IO.encoding, hilited: ""};
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	if (defined(JSDOC.PluginManager)) {
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		JSDOC.PluginManager.run("onPublishSrc", src);
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	}
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	if (src.hilited) {
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		IO.saveFile(srcDir, name+publish.conf.ext, src.hilited);
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	}
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}
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/** Build output for displaying function parameters. */
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function makeSignature(params) {
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	if (!params) return "()";
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	var signature = "("
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	+
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	params.filter(
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		function($) {
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			return $.name.indexOf(".") == -1; // don't show config params in signature
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		}
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	).map(
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		function($) {
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			return $.name;
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		}
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	).join(", ")
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	+
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	")";
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	return signature;
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}
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/** Find symbol {@link ...} strings in text and turn into html links */
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function resolveLinks(str, from) {
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	str = str.replace(/\{@link ([^} ]+) ?\}/gi,
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		function(match, symbolName) {
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			return new Link().toSymbol(symbolName);
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		}
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	);
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	return str;
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}