#!/usr/bin/php
<?php
/*
PHPDoctor: The PHP Documentation Creator
Copyright (C) 2004 Paul James <paul@peej.co.uk>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

define('VERSION', '1.4');

if (!defined('T_COMMENT') || !extension_loaded('tokenizer') || version_compare(phpversion(), '4.3.0', '<')) {
	error('You need PHP version 4.3.0 or greater with the "tokenizer" extension to run this script, please upgrade');
	exit;
}


if (!isset($argv[0])) { // not being run command line
	error('This program must be run from the command line using the CLI version of PHP');
	exit;
} elseif (!isset($argv[1])) { // use default config file
	if (is_file('default.ini')) {
		warning('Using default config file "default.ini"');
		$argv[1] = 'default.ini';
	} else {
		error('Usage: phpdoc.php [config_file]');
		exit;
	}
}

/** Path PHPDoctor is running from */
define('PATH', dirname($argv[0]));

/** Default template path */
define('DEFAULT_TEMPLATE', 'templates/default');

// read config file
if (is_file($argv[1])) {
	$settings = @parse_ini_file($argv[1]);
	if (count($settings) == 0) {
		error('Could not parse configuration file "'.$argv[1].'"');
		exit;
	}
} else {
	error('Could not find configuration file "'.$argv[1].'"');
	exit;
}

// record start time
$startTime = getTime();

// set config directives
if (isset($settings['files'])) $in_file = $settings['files'];
if (isset($settings['file_path'])) {
	define('FILE_PATH', prefixFilename('', $settings['file_path']));
} else {
	define('FILE_PATH', prefixFilename('', dirname($argv[1])));
}
if (isset($settings['output_dir'])) {
	define('OUT_DIR', prefixFilename(pathAppendSlash($settings['output_dir']), FILE_PATH));
} else {
	define('OUT_DIR', prefixFilename('apidocs/', FILE_PATH));
}
if (isset($settings['title'])) define('LONG_TITLE', $settings['title']); else define('LONG_TITLE', 'Noname');
if (isset($settings['short_title'])) define('SHORT_TITLE', $settings['short_title']); else define('SHORT_TITLE', LONG_TITLE);
if (isset($settings['subdirs'])) define('SUBDIRS', $settings['subdirs']); else define('SUBDIRS', FALSE);
if (isset($settings['file_list'])) define('FILE_LIST', $settings['file_list']);
if (isset($settings['template'])) define('TEMPLATE', 'templates/'.$settings['template']); else define('TEMPLATE', DEFAULT_TEMPLATE);
if (isset($settings['globals'])) define('NO_GLOBAL', !$settings['globals']); else define('NO_GLOBAL', FALSE);
if (isset($settings['constants'])) define('NO_CONSTANT', !$settings['constants']); else define('NO_CONSTANT', FALSE);
if (isset($settings['tree'])) define('NO_TREE', !$settings['tree']); else define('NO_TREE', FALSE);
if (isset($settings['default_package'])) define('DEFAULT_PACKAGE', $settings['default_package']); else define('DEFAULT_PACKAGE', strtolower(SHORT_TITLE));
if (isset($settings['warnings'])) define('DISPLAY_WARNINGS', $settings['warnings']); else define('DISPLAY_WARNINGS', TRUE);
if (isset($settings['footer'])) define('FOOTER', $settings['footer']); else define('FOOTER', 'This document was generated by <a href="http://phpdoctor.sourceforge.net/">PHPDoctor: The PHP Documentation Creator</a> v'.VERSION.'.');
if (isset($settings['overview_comment'])) define('OVERVIEW_COMMENT', prefixFilename($settings['overview_comment'], FILE_PATH)); else define('OVERVIEW_COMMENT', prefixFilename('overview.html', FILE_PATH));
if (isset($settings['package_comment_dir'])) define('PACKAGE_COMMENT_DIR', prefixFilename(pathAppendSlash($settings['package_comment_dir']), FILE_PATH)); else define('PACKAGE_COMMENT_DIR', FILE_PATH);
if (isset($settings['hide_private'])) define('HIDE_PRIVATE', $settings['hide_private']); else define('HIDE_PRIVATE', FALSE);

// define tokienizer constants if not defined so we don't throw undefined constant errors later on
if (!defined('T_DOC_COMMENT')) define('T_DOC_COMMENT', 0);
if (!defined('T_ML_COMMENT')) define('T_ML_COMMENT', 0);
if (!defined('T_PRIVATE')) define('T_PRIVATE', 0);
if (!defined('T_PROTECTED')) define('T_PROTECTED', 0);
if (!defined('T_PUBLIC')) define('T_PUBLIC', 0);
if (!defined('T_ABSTRACT')) define('T_ABSTRACT', 0);
if (!defined('T_FINAL')) define('T_FINAL', 0);
if (!defined('T_INTERFACE')) define('T_INTERFACE', 0);
if (!defined('T_IMPLEMENTS')) define('T_IMPLEMENTS', 0);
if (!defined('T_CONST')) define('T_CONST', 0);

if (defined('FILE_LIST')) {
	$filename = FILE_LIST;
	echo 'Reading file list ', $filename, "...\n";
	$filename = prefixFilename($filename, FILE_PATH);
	if (!is_file($filename)) {
		error('Could not open file '.$filename);
		exit;
	}
	$files = file($filename);
	$fileList = '';
	foreach ($files as $file) {
		$fileList .= rtrim($file).',';
	}
	$fileList = substr($fileList, 0, -1);
	if (isset($in_file)) {
		$in_file .= ','.$fileList;
	} else {
		$in_file = $fileList;
	}
}

if (!isset($in_file) || $in_file == '') {
	error('No files specified to parse in config file, halting');
	exit;
}

$objects = array();
$packages = array();
$summary = array();
$classTree = array();
$interfaceTree = array();

$pos = strpos($in_file, ',');
if ($pos !== FALSE) {
	$inFiles = explode(',', $in_file);
} else {
	$inFiles = array($in_file);
}

echo 'Output directory set as ', OUT_DIR, "\n";
if (is_dir(OUT_DIR)) {
	warning('Output directory already exists, overwriting existing files.');
}
echo 'Documentation title set as ', LONG_TITLE, "\n";
echo 'Documentation short title set as ', SHORT_TITLE, "\n";
if (NO_GLOBAL) echo "Globals will not be parsed.\n";
if (NO_CONSTANT) echo "Constants will not be parsed.\n";

readFiles($inFiles, FILE_PATH);

replaceInlineLinks($objects);
setSeeLinks($objects);

//dumpToFile($objects);

foreach ($objects as $package_name => $package) {

	$package_summary = array();
	$package_classTree = array();
	$package_interfaceTree = array();

//set package dir
	$objects[$package_name]['dir'] = packageToDir($package_name);
	
	$package['package'] = $package_name;
	echo 'Writing package ', $package_name, "...\n";

	if (isset($package['params'])) {
		echo ' ', count($package['params']), " globals parsed.\n";
	}
	if (isset($package['constants'])) {
		echo ' ', count($package['constants']), " constants parsed.\n";
	}
	if (isset($package['classes'])) {
		echo ' ', count($package['classes']), " classes parsed.\n";
	}
	if (isset($package['interfaces'])) {
		echo ' ', count($package['interfaces']), " interfaces parsed.\n";
	}
	if (isset($package['functions'])) {
		echo ' ', count($package['functions']), " functions parsed.\n";
	}

	if (isset($package['classes'])) { // we have classes, output them
		echo " Writing classes...\n";
		ksort($package['classes']);
		foreach ($package['classes'] as $class) {
			if (isset($class['shortDescription'])) {
				$description = $class['shortDescription'];
			} else {
				$description = 'No description';
			}
			addToSummary($package_summary, 'classes', $class['name'], $description, $package_name);
			if (isset($class['extends'])) {
				addToTree($package_classTree, $class['name'], $package_name, $class['extends']);
			} else {
				addToTree($package_classTree, $class['name'], $package_name);
			}
			echo '  Writing ', $class['name'], "\n";
			$classDetails = array('this' => &$class);
			if (isset($class['extends'])) {
				getParentsDetails('classes', $class['extends'], $classDetails, $objects);
			}
			if (isset($class['implements'])) {
				foreach ($class['implements'] as $interface) {
					getParentsDetails('interfaces', $interface, $classDetails, $objects);
				}
			}
			$contents = plugTemplate($classDetails, 'class', $package_name);
			writeFile($contents, $class['name'].'.html', $package_name);
		}
	}

	if (isset($package['interfaces'])) { // we have interfaces, output them
		echo " Writing interfaces...\n";
		ksort($package['interfaces']);
		foreach ($package['interfaces'] as $interface) {
			if (isset($interface['shortDescription'])) {
				$description = $interface['shortDescription'];
			} else {
				$description = 'No description';
			}
			addToSummary($package_summary, 'interfaces', $interface['name'], $description, $package_name);
			if (isset($interface['extends'])) {
				addToTree($package_interfaceTree, $interface['name'], $package_name, $interface['extends']);
			} else {
				addToTree($package_interfaceTree, $interface['name'], $package_name);
			}
			echo '  Writing ', $interface['name'], "\n";
			$interfaceDetails = array('this' => &$interface);
			if (isset($interface['extends'])) {
				getParentsDetails('interfaces', $interface['extends'], $interfaceDetails, $objects);
			}
			if (isset($interface['implements'])) {
				foreach ($interface['implements'] as $inter) {
					getParentsDetails('interfaces', $inter, $interfaceDetails, $objects);
				}
			}
			$contents = plugTemplate($interfaceDetails, 'interface', $package_name);
			writeFile($contents, $interface['name'].'.html', $package_name);
		}
	}

	if (isset($package['functions'])) { // we have functions, output them
		echo " Writing functions...\n";
		ksort($package['functions']);
		foreach ($package['functions'] as $function) {
			if (isset($function['shortDescription'])) {
				$description = $function['shortDescription'];
			} else {
				$description = 'No description';
			}
			addToSummary($package_summary, 'functions', $function['name'], $description, $package_name);
		}
		$contents = plugTemplate($package['functions'], 'package-functions', $package_name);
		writeFile($contents, 'package-functions.html', $package_name);
	}

	if (isset($package['params'])) { // we have globals, output them
		echo " Writing globals...\n";
		ksort($package['params']);
		foreach ($package['params'] as $key => $global) {
			foreach ($global as $key2 => $item) { // since we can have multiple occurances of the same global, we'll pick it up more than once, so we have to consolidate these occurances into a single item
				if (is_array($item) && isset($item[0])) {
					$global[$key2] = $item[0];
					$package['params'][$key][$key2] = $item[0];
				}
			}
			if (isset($global['shortDescription'])) {
				$description = $global['shortDescription'];
			} else {
				$description = 'No description';
			}
			addToSummary($package_summary, 'globals', $global['name'], $description, $package_name);
		}
		$contents = plugTemplate($package['params'], 'package-globals', $package_name);
		writeFile($contents, 'package-globals.html', $package_name);
	}

	if (isset($package['constants'])) { // we have globals, output them
		echo " Writing constants...\n";
		ksort($package['constants']);
		foreach ($package['constants'] as $constant) {
			if (isset($constant['shortDescription'])) {
				$description = $constant['shortDescription'];
			} else {
				$description = 'No description';
			}
			addToSummary($package_summary, 'constants', $constant['name'], $description, $package_name);
		}
		$contents = plugTemplate($package['constants'], 'package-constants', $package_name);
		writeFile($contents, 'package-constants.html', $package_name);
	}

	echo " Writing package summary...\n";
	echo "  DEBUG: package_name: " . PACKAGE_COMMENT_DIR.$package_name.'.html' . "\n";
	$comment_file = PACKAGE_COMMENT_DIR.$package_name.'.html';
	if (is_file($comment_file)) {
		echo ' Reading package comment file ', $comment_file, "\n";
		$comment = getHTMLContents($comment_file);
	} else {
		$comment = FALSE;
	}
	$contents = plugTemplate($package, 'package-summary', $package_name, $comment);
	writeFile($contents, 'package-summary.html', $package_name);

	echo " Writing package index...\n";
	$contents = plugTemplate($package_summary, 'package-frame', $package_name);
	writeFile($contents, 'package-frame.html', $package_name);

	if (!NO_TREE) {
		echo " Writing package class tree...\n";
		$tree = array('classes' => &$package_classTree, 'interfaces' => &$package_interfaceTree);
		$contents = plugTemplate($tree, 'package-tree', $package_name);
		writeFile($contents, 'package-tree.html', $package_name);
	}

	$summary = mergeArrays($summary, $package_summary);
	$classTree = mergeArrays($classTree, $package_classTree);
	$interfaceTree = mergeArrays($interfaceTree, $package_interfaceTree);

}

// write indexes and stuff

echo "Writing package list...\n";
$contents = plugTemplate($objects, 'overview-frame', FALSE);
writeFile($contents, 'overview-frame.html');

echo "Writing overview summary...\n";
if (is_file(OVERVIEW_COMMENT)) {
	echo ' Reading overview file ', OVERVIEW_COMMENT, "\n";
	$comment = getHTMLContents(OVERVIEW_COMMENT);
} else {
	$comment = FALSE;
}
$contents = plugTemplate($objects, 'overview-summary', FALSE, $comment);
writeFile($contents, 'overview-summary.html');

echo "Writing overview index...\n";
$contents = plugTemplate($summary, 'package-frame', FALSE);
writeFile($contents, 'allitems-frame.html');

if (NO_TREE) {
	echo "Not generating class tree\n";
} else {
	echo "Writing class tree...\n";
	$tree = array('classes' => &$classTree, 'interfaces' => &$interfaceTree);
	$contents = plugTemplate($tree, 'overview-tree', FALSE);
	writeFile($contents, 'overview-tree.html');
}

echo "Writing frameset...\n";
$contents = plugTemplate($summary, 'index', FALSE);
writeFile($contents, 'index.html');

echo "Copying stylesheet...\n";
copy(PATH.'/'.getTemplateFile('stylesheet.css'), OUT_DIR.'stylesheet.css');

echo "Done\n";
echo 'Documentation generated in ', round(getTime() - $startTime, 2), " seconds\n";

/**
 * Read input files and parse them into tokens. This function is
 * recursively called by itself if PHPDoctor is searching sub
 * directories.
 *
 * @param array inFiles Array of input files to parse
 */
function readFiles($inFiles, $dir) {
	global $objects, $tokens;

	foreach ($inFiles as $filename) {
		$filename = prefixFilename($filename, $dir);
		if (!is_file($filename)) {
			$globResults = glob(str_replace('\\', '/', $filename)); // switch slashes since old versions of glob need forward slashes
			if ($globResults) {
				foreach ($globResults as $filename) {
					if (!is_dir($filename)) {
						echo 'Reading file ', $filename, "\n";
						$fileString = @file_get_contents($filename);
						if ($fileString) {
							$tokens = token_get_all($fileString);
							$objects = mergeArrays($objects, parseTokens($tokens));
						} else {
							error('Could not read file '.$filename);
						}
					}
				}
			} else {
				if (!SUBDIRS) {
					error('Could not find file '.$filename);
				}
			}
		} else {
			echo 'Reading file ', $filename, "\n";
			$fileString = @file_get_contents($filename);
			if ($fileString) {
				$tokens = token_get_all($fileString);
				$objects = mergeArrays($objects, parseTokens($tokens));
			} else {
				error('Could not read file '.$filename);
			}
		}
	}

	if (SUBDIRS) { // recurse into subdir
		$globResults = glob($dir.'*', GLOB_ONLYDIR); // get subdirs
		if ($globResults) {
			foreach ($globResults as $filename) {
				echo 'Reading directory ', $filename, "...\n";
				readFiles($inFiles, $filename);
			}
		}
	}
}

/**
 * Write doc tags to output. Doc tag results are encased in HTML definition list tags.
 *
 * @param array object Object to write tags for
 */
function writeTags(&$object) {
	if (isset($object['params'])) {
		echo '<dl><dt>Parameters:</dt>';
		foreach ($object['params'] as $param) {
			if (isset($param['name'])) {
				echo '<dd><code>', $param['name'], '</code>';
				if (isset($param['description'])) {
					echo ' - ', $param['description'], '</dd>';
				}
			}
		}
		echo '</dl>';
	}
	if (isset($object['author'])) {
		echo '<dl><dt>Author:</dt><dd>';
		echo join(', ', $object['author']);
		echo '</dd></dl>';
	}
	if (isset($object['deprecated'])) {
		echo '<dl><dt>Deprecated:</dt><dd>';
		echo join(', ', $object['deprecated']);
		echo '</dd></dl>';
	}
	if (isset($object['return']['description'])) {
		echo '<dl><dt>Returns:</dt><dd>', $object['return']['description'], '</dd></dl>';
	}
	if (isset($object['see'])) {
		echo '<dl><dt>See Also:</dt><dd>';
		echo join(', ', $object['see']);
		echo '</dd></dl>';
	}
	if (isset($object['since'])) {
		echo '<dl><dt>Since:</dt><dd>';
		echo join(', ', $object['since']);
		echo '</dd></dl>';
	}
	if (isset($object['version'])) {
		echo '<dl><dt>Version:</dt><dd>';
		echo join(', ', $object['version']);
		echo '</dd></dl>';
	}
}

/**
 * Get the details of the classes parent from the objects array. This function
 * recursively calls itself to get parents details.
 *
 * @param str type Type of object we are dealing with
 * @param str parent Name of parent class
 * @param array classDetails
 * @param array objects
 */
function getParentsDetails($type, $parent, &$classDetails, &$objects) {
	if (!isset($classDetails[$parent])) {
		foreach ($objects as $package) { // search through packages for parent class
			if (isset($package[$type][$parent])) {
				$classDetails[$parent] = $package[$type][$parent];
			}
		}
		if (!isset($classDetails[$parent])) { // parent has not been parsed, add dummy entry
			// not implemented, not sure whether we'll really need this yet
		}
		if (isset($classDetails[$parent]['extends'])) {
			getParentsDetails($type, $classDetails[$parent]['extends'], $classDetails, $objects);
		}
		if (isset($classDetails[$parent]['implements'])) {
			foreach ($classDetails[$parent]['implements'] as $interface) {
				getParentsDetails('interfaces', $interface, $classDetails, $objects);
			}
		}
	}
}

/**
 * Plug values into a template file.
 *
 * @param array t Template items
 * @param str template Name of template to use
 * @return str The template with the values plugged in
 */
function &plugTemplate(&$t, $template, $package_name = NULL, $comment = FALSE) {
	if (isset($package_name) && $package_name) { // get package name and calculate directory depth this template will be placed at
		$package_dir = packageToDir($package_name).'/';
		$link_path = '../';
		$depth = substr_count($package_dir, '/');
		for ($foo = 1; $foo < $depth; $foo++) {
			$link_path .= '../';
		}
	} elseif (isset($package_name)) { // overview template
		$package_dir = '';
		$link_path = '';
	} else { // default package
		$package_dir = '';
		$link_path = '';
		$package_name = DEFAULT_PACKAGE;
	}
	ob_start();
	include(getTemplateFile($template.'.php'));
	$contents = ob_get_contents();
	ob_end_clean();
	return $contents;
}

/**
 * Get the full path and name of a template file.
 *
 * @param str filename Name of template file to get
 * @return str The full path and name of the template file
 */
function getTemplateFile($filename) {
	if (file_exists(TEMPLATE.'/'.$filename)) { // first search in defined templates directory
		return TEMPLATE.'/'.$filename;
	} else { // use default template
    return DEFAULT_TEMPLATE.'/'.$filename;
	}
}

/**
 * Write a warning message to standard output.
 *
 * @param str msg Warning message to output
 */
function warning($msg) {
	if (!defined('DISPLAY_WARNINGS') || DISPLAY_WARNINGS)
		fwrite(STDERR, 'WARNING: '.$msg."\n");
}

/**
 * Write an error message to standard output.
 *
 * @param str msg Error message to output
 */
function error($msg) {
	fwrite(STDERR, 'ERROR: '.$msg."\n");
}

/**
 * Write a file given contents and a filename
 *
 * @param str contents Content to write
 * @param str filename File to write to
 * @param str package Package to write file into
 */
function writeFile($contents, $filename, $package = NULL) {
	if ($package) {
		$dir = OUT_DIR.packageToDir($package);
	} else {
		$dir = OUT_DIR;
	}
	if (!is_dir($dir)) {
		makeDir($dir);
	}
	$fp = fopen($dir.'/'.$filename, 'w');
	if ($fp) {
		fwrite($fp, $contents);
	}
}

/** Turn a package name into the package directory name */
function packageToDir($package) {
	$package = str_replace('\\', '/', $package);
	$package = str_replace('.', '/', $package);
	return $package;
}

/** Make a directory and all parents as needed */
function makeDir($dir) {
	$dirs = explode('/', $dir);
	$dir_to_make = FALSE;
	foreach($dirs as $dir) {
		if ($dir_to_make) {
			$dir_to_make .= '/'.$dir;
		} else {
			$dir_to_make = $dir;
		}
		if (!is_dir($dir_to_make)) mkdir($dir_to_make);
	}
}

/**
 * Add a classes details to the tree generator array.
 *
 * @param array tree Tree generator array
 * @param str name Name of class to add
 * @param str extends Name of parent of class to add
 */
function addToTree(&$tree, $name, $package, $extends = NULL) {
	if (is_array($name)) $name = $name[0];
	$array['name'] = $name;
	$array['package'] = $package;
	$array['extends'] = $extends;
	$array['dir'] = packageToDir($package);
	$tree[$name] = $array;	
}

/**
 * Add an objects details to the summary generator array.
 *
 * @param array summary Summary generator array
 * @param str type Type of object to add
 * @param str name Name of object to add
 * @param str description Description of object to add
 */
function addToSummary(&$summary, $type, $name, $description, $package) {
	if (is_array($name)) $name = $name[0];
	$array['name'] = $name;
	$array['shortDescription'] = $description;
	$array['package'] = $package;
	$array['dir'] = packageToDir($package);
	$summary[$type][$name] = $array;
}

/**
 * Turn a link doc tag into a URI.
 *
 * @param str link Link to process
 * @return str The text with the links processed
 */
function parseLink($link, $packageName = DEFAULT_PACKAGE) {
	global $objects;
	
	$objectName = FALSE;
	$itemName = FALSE;
	
	$root = substr_count($packageName, '.');
	$root = str_repeat('../', $root + 1);
	
	$link = preg_replace('/\(.*\)/U', '', $link); // remove parameters
	
	$pos = strpos($link, ' ');
	if ($pos !== FALSE) {
		$obj = substr($link, 0, $pos);
		$label = substr($link, $pos);
	} else {
		$obj = $link;
	}

	$pos = strrpos($obj, '.');
	if ($pos !== FALSE) { // get package name
		$packageName = substr($obj, 0, $pos);
		$obj = substr($obj, $pos + 1);
	}

	$packageDir = packageToDir($packageName);
	
	$pos = strpos($obj, '::');
	$pos2 = strpos($obj, '#');
	if (preg_match('/<a href=".*">.*<\/a>/', $link)) {
		return $link;
	} elseif ($pos !== FALSE) {
		$objectName = substr($obj, 0, $pos);
		$itemName = substr($obj, $pos + 2);
	} elseif ($pos2 !== FALSE) {
		$objectName = substr($obj, 0, $pos2);
		$itemName = substr($obj, $pos2 + 1);
	} else {
		$itemName = $obj;
	}
	
	if (!isset($label)) {
		if ($objectName) {
			$label = $objectName.'::'.$itemName;
		} else {
			$label = $itemName;
		}
	}

	if (isset($objects[$packageName]['classes'][$objectName]['functions'][$itemName]) || isset($objects[$packageName]['interfaces'][$objectName]['functions'][$itemName])) {
		return '<a href="'.$root.$packageDir.'/'.$objectName.'.html#'.$itemName.'">'.$label.'</a>';
	} elseif (isset($objects[$packageName]['classes'][$itemName]) || isset($objects[$packageName]['interfaces'][$itemName])) {
		return '<a href="'.$root.$packageDir.'/'.$itemName.'.html">'.$label.'</a>';
	} elseif (isset($objects[$packageName]['functions'][$itemName])) {
		return '<a href="'.$root.$packageDir.'/package-functions.html#'.$itemName.'">'.$label.'</a>';
	} elseif (isset($objects[$packageName]['constants'][$itemName])) {
		return '<a href="'.$root.$packageDir.'/package-constants.html#'.$itemName.'">'.$label.'</a>';
	} elseif (isset($objects[$packageName]['globals'][$itemName])) {
		return '<a href="'.$root.$packageDir.'/package-globals.html#'.$itemName.'">'.$label.'</a>';
	}
	return '"'.$link.'"';
}

/**
 * Replace inline link doc tags with HTML tags. This function recursively traverses an array looking for description entries to parse for link tags.
 *
 * @param array items Object array to traverse for links
 * @return array The parsed array
 */
function replaceInlineLinks(&$items, $packageName = DEFAULT_PACKAGE) {
	foreach ($items as $key => $item) {
		if (isset($items['package']) && !is_array($items['package'])) {
			$packageName = $items['package'];
		}
		if (is_array($item)) {
			$items[$key] = replaceInlineLinks($item, $packageName);
		} elseif ($key == 'shortDescription' || $key == 'description') {
			$text = $item;
			$matches = array();
			preg_match_all('/{@link .*}/U', $text, $matches, PREG_OFFSET_CAPTURE | PREG_PATTERN_ORDER);
			if (isset($matches[0]) && count($matches[0]) > 0) {
				$newtext = '';
				$lastPos = 0;
				foreach ($matches[0] as $match) {
					$link = substr($match[0], 7, strlen($match[0]) - 8);
					$newtext .= substr($text, $lastPos, $match[1] - $lastPos).'<code>'.parseLink($link, $packageName).'</code>';
					$lastPos = $match[1] + strlen($match[0]);
				}
				$text = $newtext.substr($text, $lastPos);
			}
			$matches = array();
			preg_match_all('/{@linkplain .*}/U', $text, $matches, PREG_OFFSET_CAPTURE | PREG_PATTERN_ORDER);
			if (isset($matches[0]) && count($matches[0]) > 0) {
				$newtext = '';
				$lastPos = 0;
				foreach ($matches[0] as $match) {
					$link = substr($match[0], 12, strlen($match[0]) - 13);
					$newtext .= substr($text, $lastPos, $match[1] - $lastPos).parseLink($link, $packageName);
					$lastPos = $match[1] + strlen($match[0]);
				}
				$text = $newtext.substr($text, $lastPos);
			}
			$items[$key] = $text;
		}
	}
	return $items;
}

/**
 * Replace see doc tags with HTML tags. This function recursively traverses an array looking for see entries to convert.
 *
 * @param array items Object array to traverse for links
 * @return array The parsed array
 */
function setSeeLinks(&$items) {
	foreach ($items as $key => $item) {
		if ($key === 'see' && is_array($item)) {
			if (isset($items['package']) && !is_array($items['package'])) {
				$packageName = $items['package'];
			} else {
				$packageName = DEFAULT_PACKAGE;
			}
			foreach ($item as $seekey => $see) {
				$items[$key][$seekey] = parseLink(trim($see), $packageName);
			}
		} elseif (is_array($item)) {
			$items[$key] = setSeeLinks($item);
		}
	}
	return $items;
}

/**
 * Parse the token array into objects.
 *
 * @param array tokens Token array
 * @return array Object array
 */
function parseTokens(&$tokens) {
	
	echo "Parsing tokens...\n";

	$objects = array();
	$docComment = array();
	
	$access = 'public';
	$abstract = FALSE;
	$final = FALSE;
	$static = FALSE;
	$var = FALSE;
	$const = FALSE;

	$object = &$objects[];
	$object['inBody'] = 0;
	$open_curly_braces = FALSE;
	$in_parsed_string = FALSE;

	foreach ($tokens as $key => $token) {
		if (!$in_parsed_string && is_array($token)) {
			switch ($token[0]) {

			case T_COMMENT: // read comment
			case T_ML_COMMENT: // and multiline comment (deprecated I think)
			case T_DOC_COMMENT: // and catch PHP5 doc comment token too
				$result = processDocComment($token[1]);
				if ($result) $docComment = mergeArrays($docComment, $result);
				break;

			case T_CLASS: // read class
				$subObject = array();
				$subObject['..'] = &$object;
				$subObject['package'] = DEFAULT_PACKAGE;
				$subObject['name'] = getNext($tokens, $key, T_STRING);
				$subObject['abstract'] = $abstract;
				$subObject['final'] = $final;
				$subObject['docComment'] = $docComment;
				if (isset($docComment['package'])) $subObject['package'] = $docComment['package'];
				$subObject['dir'] = packageToDir($subObject['package']);
				$object = &$object[$subObject['package']]['classes'][$subObject['name']];
				if ($object) {
					$object = array_merge($object, $subObject);
				} else {
					$object = $subObject;
				}
				$docComment = array();
				$abstract = FALSE;
				$final = FALSE;
				break;
			case T_INTERFACE: // read interface
				$subObject = array();
				$subObject['..'] = &$object;
				$subObject['package'] = DEFAULT_PACKAGE;
				$subObject['name'] = getNext($tokens, $key, T_STRING);
				$subObject['abstract'] = $abstract;
				$subObject['final'] = $final;
				$subObject['docComment'] = $docComment;
				if (isset($docComment['package'])) $subObject['package'] = $docComment['package'];
				$subObject['dir'] = packageToDir($subObject['package']);
				$object = &$object[$subObject['package']]['interfaces'][$subObject['name']];
				if ($object) {
					$object = array_merge($object, $subObject);
				} else {
					$object = $subObject;
				}
				$docComment = array();
				$abstract = FALSE;
				$final = FALSE;
				break;
			case T_EXTENDS: // get extends clause
				$object['extends'] = getNext($tokens, $key, T_STRING);
				break;
			case T_IMPLEMENTS: // get implements clause
				while($tokens[++$key] != '{') {
					if ($tokens[$key][0] == T_STRING) {
						$object['implements'][] = $tokens[$key][1];
					}
				}
				break;

			case T_PRIVATE:
				$access = 'private';
				break;
			case T_PROTECTED:
				$access = 'protected';
				break;
			case T_ABSTRACT:
				$abstract = TRUE;
				break;
			case T_FINAL:
				$final = TRUE;
				break;
			case T_STATIC:
				$static = TRUE;
				break;
			case T_VAR:
				$var = TRUE;
				break;
			case T_CONST:
				$const = TRUE;
				break;

			case T_FUNCTION: // read function
				$subObject = array();
				$subObject['..'] = &$object;
				if (!isset($object['name'])) { // only set package name for top level functions
					$subObject['package'] = DEFAULT_PACKAGE;
				}
				$subObject['name'] = getNext($tokens, $key, T_STRING);
				$subObject['access'] = $access;
				if (substr($subObject['name'], 0, 1) == '_' && $subObject['access'] == 'public') $subObject['access'] = 'private';
				$subObject['abstract'] = $abstract;
				$subObject['final'] = $final;
				$subObject['static'] = $static;
				$subObject['return']['type'] = 'void';
				$subObject['docComment'] = $docComment;
				if (isset($docComment['package'])) $subObject['package'] = $docComment['package'];
				if (!HIDE_PRIVATE || ($subObject['access'] != 'private' && (!isset($docComment['access']) || $docComment['access'] != 'private'))) {
					if (isset($subObject['package'])) {
						$subObject['dir'] = packageToDir($subObject['package']);
						$object = &$object[$subObject['package']]['functions'][$subObject['name']];
					} else {
						$object = &$object['functions'][$subObject['name']];
					}
					if ($object) {
						$object = array_merge($object, $subObject);
					} else {
						$object = $subObject;
					}
				}
				$docComment = array();
				$access = 'public';
				$abstract = FALSE;
				$final = FALSE;
				$static = FALSE;
				break;

			case T_STRING:
				if (!NO_CONSTANT && $token[1] == 'define') { // read global constant
					$subObject = array();
					if (!isset($object['classes']) || !isset($object['interfaces'])) { // only set package name for top level functions
						$subObject['package'] = DEFAULT_PACKAGE;
					}
					$subObject['name'] = trim(getNext($tokens, $key, T_CONSTANT_ENCAPSED_STRING), '\'"');
					$subObject['type'] = 'const';
					addDocComment($subObject, $docComment);
					if (isset($docComment['package'])) $subObject['package'] = $docComment['package'];
					if (isset($subObject['package'])) {
						$subObject['dir'] = packageToDir($subObject['package']);
						if (isset($object['params'][$subObject['name']])) {
							$object[$subObject['package']]['constants'][$subObject['name']] = array_merge($object['params'][$subObject['name']], $subObject);
						} else {
							$object[$subObject['package']]['constants'][$subObject['name']] = $subObject;
						}
					} else {
						if (isset($object['params'][$subObject['name']])) {
							$object['constants'][$subObject['name']] = array_merge($object['params'][$subObject['name']], $subObject);
						} else {
							$object['constants'][$subObject['name']] = $subObject;
						}
					}
					$docComment = array();
				} elseif ($const) { // member constant
					$subObject = array();
					$subObject['final'] = $final;
					$subObject['static'] = $static;
					$subObject['type'] = 'const';
					addDocComment($subObject, $docComment);
					do {
						if ($tokens[$key][0] == T_STRING) {
							$subObject['access'] = $access;
							$subObject['name'] = $tokens[$key][1];
							$object['vars'][] = $subObject;
						}
						$key++;
					} while($tokens[$key] != ';');
					$docComment = array();
					$final = FALSE;
					$static = FALSE;
					$const = FALSE;
				}
				break;

			case T_VARIABLE: // read variables / parameters
				if ($var || $access == 'private' || $access == 'protected') { // member var
					$subObject = array();
					$subObject['final'] = $final;
					$subObject['static'] = $static;
					$subObject['type'] = 'var';
					$subObject['default'] = '';
					addDocComment($subObject, $docComment);
					$default = FALSE;
					do {
						$key++;
						if ($tokens[$key] == '=') {
							$default = TRUE;
						} elseif ($tokens[$key] == ',' || $tokens[$key] == ';') {
							$subObject['access'] = $access;
							$subObject['name'] = getPrev($tokens, $key, T_VARIABLE);
							if (substr($subObject['name'], 1, 1) == '_' && $subObject['access'] == 'public') $subObject['access'] = 'private';
							$subObject['default'] = trim($subObject['default']);
							if (!HIDE_PRIVATE || $subObject['access'] != 'private') {
								$object['vars'][] = $subObject;
							}
							$subObject['default'] = '';
							$default = FALSE;
						} elseif($default) {
							if (is_array($tokens[$key])) {
								$subObject['default'] .= $tokens[$key][1];
							} else {
								$subObject['default'] .= $tokens[$key];
							}
						}
					} while($tokens[$key] != ';');
					$docComment = array();
					$access = 'public';
					$final = FALSE;
					$static = FALSE;
					$var = FALSE;
				} elseif ((!isset($object['inBody']) || $object['inBody'] == 0) && (!NO_GLOBAL || isset($object['..']))) {
					$subObject = array();
					if (!isset($object['name'])) { // only set package name for top level functions
						$subObject['package'] = DEFAULT_PACKAGE;
					}
					$subObject['name'] = $tokens[$key][1];
					if (isset($tokens[$key - 1][0]) && is_array($tokens[$key - 2]) && $tokens[$key - 2][0] == T_STRING && $tokens[$key - 1][0] == T_WHITESPACE) {
						$subObject['type'] = $tokens[$key - 2][1];
					} else {
						$subObject['type'] = 'var';
					}
					addDocComment($subObject, $docComment);
					if ($tokens[$key + 1] == '=' || $tokens[$key + 2] == '=') {
						$subObject['default'] = '';
						$key2 = $key + 1;
						do {
							if (is_array($tokens[$key2])) {
								if ($tokens[$key2][1] != '=') $subObject['default'] .= $tokens[$key2][1];
							} else {
								if ($tokens[$key2] != '=') $subObject['default'] .= $tokens[$key2];
							}
							$key2++;
						} while(isset($tokens[$key2]) && $tokens[$key2] != ';' && $tokens[$key2] != ',' && $tokens[$key2] != ')');
						$subObject['default'] = trim($subObject['default'], ' ()');
					}
					if (isset($docComment['package'])) $subObject['package'] = $docComment['package'];
					if (isset($subObject['package'])) {
						$subObject['dir'] = packageToDir($subObject['package']);
						if (isset($object['params'][substr($tokens[$key][1], 1)])) {
							$object[$subObject['package']]['params'][substr($tokens[$key][1], 1)] = array_merge($subObject, $object['params'][substr($tokens[$key][1], 1)]);
						} else {
							$object[$subObject['package']]['params'][substr($tokens[$key][1], 1)] = $subObject;
						}
					} else {
						if (isset($object['params'][substr($tokens[$key][1], 1)])) {
							$object['params'][substr($tokens[$key][1], 1)] = array_merge($subObject, $object['params'][substr($tokens[$key][1], 1)]);
						} else {
							$object['params'][substr($tokens[$key][1], 1)] = $subObject;
						}
					}
					$docComment = array();
				}
				break;

			case T_CURLY_OPEN:
			case T_DOLLAR_OPEN_CURLY_BRACES: // we must catch this so we don't accidently step out of the current block
				$open_curly_braces = TRUE;
				break;
			}

		} else {
			switch ($token) {
			case '{':
				if (!$in_parsed_string) {
					if (!isset($object['inBody'])) $object['inBody'] = 0;
					$object['inBody']++;
				}
				break;
			case '}':
				if (!$in_parsed_string) {
					if ($open_curly_braces) { // end of var curly brace syntax
						$open_curly_braces = FALSE;
					} else {
						$object['inBody']--;
						if ($object['inBody'] == 0 && isset($object['..'])) {
							addDocComment($object, $object['docComment']);
							$object = &$object['..'];
							$docComment = array();
							$access = 'public';
							$abstract = FALSE;
							$final = FALSE;
							$static = FALSE;
						}
					}
				}
				break;
			case ';': // case for closing abstract functions
				if (!$in_parsed_string && !isset($object['inBody'])) {
					addDocComment($object, $object['docComment']);
					$object = &$object['..'];
					$docComment = array();
					$access = 'public';
					$abstract = FALSE;
					$final = FALSE;
					$static = FALSE;
				}
				break;
			case '"': // catch parsed strings so as to ignore tokens within
				$in_parsed_string = !$in_parsed_string;
				break;
			}
		}
	}
	//print_r(get_defined_constants());
	//dumpToFile($tokens);
	//dumpToFile($objects);
	return cleanObjectArray($objects[0]);
}

/**
 * Get next token of a certain type from token array
 *
 * @param array tokens Token array to search
 * @param int key Key to start searching from
 * @param int whatToGet Type of token to look for
 * @return str Value of found token
 */
function getNext(&$tokens, $key, $whatToGet) {
	$key++;
	while(!is_array($tokens[$key]) || $tokens[$key][0] != $whatToGet) {
		$key++;
		if (!isset($tokens[$key])) return FALSE;
	}
	return $tokens[$key][1];
}

/**
 * Get previous token of a certain type from token array
 *
 * @param array tokens Token array to search
 * @param int key Key to start searching from
 * @param int whatToGet Type of token to look for
 * @return str Value of found token
 */
function getPrev(&$tokens, $key, $whatToGet) {
	$key--;
	while(!is_array($tokens[$key]) || $tokens[$key][0] != $whatToGet) {
		$key--;
		if (!isset($tokens[$key])) return FALSE;
	}
	return $tokens[$key][1];
}

/**
 * Clean up object array after generation. This function removes work fields from the array.
 *
 * @param array items Object array to tidy
 * @return Tidied object array
 */
function cleanObjectArray($items) {
	if (is_array($items)) {
		foreach ($items as $key => $item) {
			if ($key === 'inBody' || $key === '..' || $key === 'docComment') {
				unset($items[$key]);
			} else {
				$items[$key] = cleanObjectArray($item);
			}
		}
	}
	return $items;
}

/**
 * Turn an array into a space seperated string
 *
 * @param array array Array to turn into a string
 * @param int startIndex Ignore items before this index
 */
function arrayToString(&$array, $startIndex) {
	$string = '';
	foreach ($array as $index => $item) {
		if ($index >= $startIndex) $string .= $item.' ';
	}
	return $string;
}

/**
 * Process a doc comment into a doc tag array.
 *
 * @param str comment The comment to process
 * @return array Array of doc comment data
 */
function processDocComment($comment) {
	$docComment = array();
	$comment = explode("\n", $comment);
	if (substr(trim($comment[0]), 0, 3) != '/**') return FALSE;

	$tagName = 'shortDescription';
	$paramName = FALSE;
	$tagIndex = FALSE;

	foreach ($comment as $line) {
		$line = trim($line, "\t\r /*"); // strip whitespace and asterix's from beginning
		$words = array();
		foreach (explode(' ', $line) as $word) { // explode line into words and eat whitespace
			if ($word != '') $words[] = trim($word, "\t ");
		}
		if (isset($words[0])) {
			
			if (substr($words[0], 0, 1) == '@') { // first word is tag
				$tagName = $words[0]; // set tag name
				$paramName = FALSE;
				$tagIndex = FALSE;
			}
			
			switch ($tagName) { // get tag contents

			case '@package':
				if (isset($words[1])) $docComment['package'] = rtrim(arrayToString($words, 1));
				break;

			case '@access':
				if (isset($words[1])) $docComment['access'] = $words[1];
				break;

			case '@param':
				if ($paramName && isset($docComment['params'][$paramName]['description'])) {
					$docComment['params'][$paramName]['description'] .= arrayToString($words, 0);
				} elseif (isset($words[2])) {
					if (substr($words[2], 0, 1) == '$') {
						$paramName = substr($words[2], 1);
					} elseif (substr($words[2], 0, 2) == '&$') {
						$paramName = substr($words[2], 2);
					} else {
						$paramName = $words[2];
					}
					$docComment['params'][$paramName]['name'] = $paramName;
					$docComment['params'][$paramName]['type'] = $words[1];
					if (isset($words[3])) $docComment['params'][$paramName]['description'] = arrayToString($words, 3);
				}
				break;

			case '@return':
				if (isset($docComment['return']['description'])) {
					$docComment['return']['description'] .= arrayToString($words, 0);
				} elseif (isset($words[1])) {
					$docComment['return']['type'] = $words[1];
					if (isset($words[2])) $docComment['return']['description'] = arrayToString($words, 2);
				}
				break;

			case '@see':
				if (isset($words[1])) $docComment['see'][] = arrayToString($words, 1);
				break;
				
			case '@var':
			case '@type':
				if (isset($docComment['type']) && isset($docComment['description'])) {
					$docComment['description'] .= arrayToString($words, 0);
				} elseif (isset($words[1])) {
					$docComment['type'] = $words[1];
					if (isset($words[2])) $docComment['description'] = arrayToString($words, 2);
				}
				break;

			case 'shortDescription':
			case 'description':
				if (!isset($docComment[$tagName])) $docComment[$tagName] = '';
				foreach ($words as $word) {
					$docComment[$tagName] .= $word.' ';
					if ($tagName == 'shortDescription') {
						if (substr($word, -1, 1) == '.') {
							$docComment['description'] = '';
							$tagName = 'description';
						}
					}
				}
				$docComment[$tagName] = $docComment[$tagName];
				break;

			default:
				$tag = substr($tagName, 1);
				if ($tagIndex && isset($docComment[$tag][$tagIndex])) {
					$docComment[$tag][$tagIndex] .= arrayToString($words, 0);
				} else {
					$docComment[$tag][] = arrayToString($words, 1);
					$tagIndex = count($docComment[$tag]);
				}
			}
		}
	}
	
	return $docComment;
}

/**
 * Add a doc comment to an object.
 *
 * @param array subObject Object to add doc comment data to
 * @param array docComment Doc comment to add
 */
function addDocComment(&$subObject, $docComment) {
	if (isset($docComment['shortDescription'])) {
		$subObject['shortDescription'] = $docComment['shortDescription'];
	}
	if (isset($docComment['description'])) {
		$subObject['description'] = $docComment['description'];
	}
	foreach ($docComment as $tag => $value) {
		if ($tag == 'params') {
			foreach($value as $name => $param) {
				if (!isset($subObject['params'][$name])) { // param doc comment found for non-defined parameter
					$warningStr = 'Unknown param "'.$name.'" found for method "';
					if (isset($subObject['..']['name'])) $warningStr .= $subObject['..']['name'].'::';
					$warningStr .= $subObject['name'].'".';
					warning($warningStr);
				}
			}
		}
		if (isset($subObject[$tag]) && is_array($value)) { // merge it
			$subObject[$tag] = mergeArrays($subObject[$tag], $value);
		} else { // just add it
			$subObject[$tag] = $value;
		}
	}
}

/**
 * Recursively merge two arrays into a single array. Same values are overwritten by the values in array two.
 *
 * @param array one Array one
 * @param array two Array two
 *
 * @return array Merged array
 */
function mergeArrays($one, $two) {
	foreach ($two as $key => $item) {
		if (isset($one[$key]) && is_array($one[$key]) && is_array($item)) {
			$one[$key] = mergeArrays($one[$key], $item);
		} else {
			$one[$key] = $item;
		}
	}
	return $one;
}

/**
 * Generate the class tree. This function is called recursively for each class with children.
 *
 * @param array t Object array
 * @param str name Name of parent class
 * @param int depth Current depth of recursion
 */
function classTree(&$t, $path, $name = NULL, $depth = 2) {
	if ($name == NULL) {
		$class = $t['this'];
	} elseif (isset($t[$name])) {
		$class = $t[$name];
	}
	if (isset($class['extends'])) {
		$depth = classTree($t, $path, $class['extends'], $depth);
	}
	if ($name == NULL) {
		echo '<strong>', $class['package'], '.', $class['name'], '</strong><br />';	
	} else {
		if (isset($class)) {
			echo '<a href="', $path, $class['dir'], '/', $class['name'], '.html">', $class['package'], '.', $class['name'], '</a><br />';
		} else {
			echo $name, '<br />';
		}
		for ($bar = 0; $bar < $depth; $bar++) echo ' ';
		echo '|<br />';
		for ($bar = 0; $bar < $depth; $bar++) echo ' ';
		echo '+--';
	}
	return $depth + 6;
}

/**
 * Recursively draw the tree for the given classes
 *
 * @param array t Array of classes to draw
 * @param str parent Name of parent node, used for recursive call
 * @param str path path to draw tree from, used in recursive call
 */
function drawTree($t, $includePackage = FALSE, $parent = NULL, $path = '') {
	$output = FALSE;
	echo '<ul>';
	foreach ($t as $class) {
		if ($class['extends'] == $parent || ($parent == NULL && !isset($t[$class['extends']]))) {
			echo '<li>';
			if ($includePackage) echo $class['package'], '.';
			echo '<a href="', $path, $class['dir'], '/', $class['name'], '.html">', $class['name'], '</a></li>';
			drawTree($t, $includePackage, $class['name'], $path);
		}
	}
	echo '</ul>';
}

/**
 * Get body of a HTML document
 *
 * @param filename
 * @return str
 */
function getHTMLContents($filename) {
		if ($contents = file_get_contents($filename)) {
			if (preg_match('/<body ?.*?>(.+)<\/body>/s', $contents, $matches)) {
				return $matches[1];
			}
		}
		warning('Could not find body in HTML file '.$filename);
		return '';
}

/**
 * Check if filename is relative, and if so prefix path
 */
function prefixFilename($filename, $path) {
		if (substr($filename, 0, 1) != '/' && substr($filename, 1, 2) != ':\\') { // if path is local, add prefix
			$path = pathAppendSlash($path);
			$filename = $path.$filename;
		}
		return $filename;
}

/**
 * Add trailing slash to path if not present
 */
function pathAppendSlash($path) {
		if (substr($path, -1, 1) != '/' && substr($path, -1, 1) != '\\') $path .= '/';
		return $path;
}

/**
 * Get the current time in microseconds
 *
 * @return int
 */
function getTime() {
	$microtime = explode(' ', microtime());
	return $microtime[0] + $microtime[1];
}

/**
 * Dump a variable to a file
 *
 * @param mixed var Variable to dump
 * @param bool append Append to existing file and continue execution
 */
function dumpToFile(&$var, $append = FALSE) { // dump parsed tokens
	if ($append) {
		$fp = fopen('output.txt', 'a');
	} else {
		$fp = fopen('output.txt', 'w');
	}
	if ($fp) {
		ob_start();
		print_r($var);
		$output = ob_get_contents();
		ob_end_clean();
		fwrite($fp, $output);
		fclose($fp);
	}
	if (!$append) die;
}

?>