Icybee / Patron

lib/markdown/markdown_extras.php

<?php
#
# Markdown Extra  -  A text-to-HTML conversion tool for web writers
#
# PHP Markdown & Extra
# Copyright (c) 2004-2012 Michel Fortin
# <http://michelf.com/projects/php-markdown/>
#
# Original Markdown
# Copyright (c) 2004-2006 John Gruber
# <http://daringfireball.net/projects/markdown/>
#

/**
 * Markdown Extra Parser Class
 */
class MarkdownExtra_Parser extends Markdown_Parser

PSR1 recommends that each class must be in a namespace of at least one level to avoid collisions.

{
	# Prefix for footnote ids.
	var $fn_id_prefix = "";

The visibility should be declared for property $fn_id_prefix.

	# Optional title attribute for footnote links and backlinks.
	var $fn_link_title = MARKDOWN_FN_LINK_TITLE;

The visibility should be declared for property $fn_link_title.

	var $fn_backlink_title = MARKDOWN_FN_BACKLINK_TITLE;

The visibility should be declared for property $fn_backlink_title.

	# Optional class attribute for footnote links and backlinks.
	var $fn_link_class = MARKDOWN_FN_LINK_CLASS;

The visibility should be declared for property $fn_link_class.

	var $fn_backlink_class = MARKDOWN_FN_BACKLINK_CLASS;

The visibility should be declared for property $fn_backlink_class.

	# Predefined abbreviations.
	var $predef_abbr = array();

The visibility should be declared for property $predef_abbr.

	function __construct() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Constructor function. Initialize the parser object.
	#
		# Add extra escapable characters before parent constructor
		# initialize the table.
		$this->escape_chars .= ':|';

		# Insert extra document, block, and span transformations.
		# Parent constructor will do the sorting.
		$this->document_gamut += array(
			//"doFencedCodeBlocks" => 5,

67% of this comment could be valid code. Did you maybe forget this after debugging?

			"stripFootnotes"     => 15,
			"stripAbbreviations" => 25,
			"appendFootnotes"    => 50,
			);
		$this->block_gamut += array(
			//"doFencedCodeBlocks" => 5,

67% of this comment could be valid code. Did you maybe forget this after debugging?

			"doTables"           => 15,
			"doDefLists"         => 45,
			);
		$this->span_gamut += array(
			"doFootnotes"        => 5,
			"doAbbreviations"    => 70,
			);

		parent::__construct();
	}


	# Extra variables used during extra transformations.
	var $footnotes = array();

The visibility should be declared for property $footnotes.

	var $footnotes_ordered = array();

The visibility should be declared for property $footnotes_ordered.

	var $abbr_desciptions = array();

The visibility should be declared for property $abbr_desciptions.

	var $abbr_word_re = '';

The visibility should be declared for property $abbr_word_re.

	# Give the current footnote number.
	var $footnote_counter = 1;

The visibility should be declared for property $footnote_counter.

	function setup() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Setting up Extra-specific variables.
	#
		parent::setup();

		$this->footnotes = array();
		$this->footnotes_ordered = array();
		$this->abbr_desciptions = array();
		$this->abbr_word_re = '';
		$this->footnote_counter = 1;

		foreach ($this->predef_abbr as $abbr_word => $abbr_desc) {
			if ($this->abbr_word_re)
				$this->abbr_word_re .= '|';
			$this->abbr_word_re .= preg_quote($abbr_word);
			$this->abbr_desciptions[$abbr_word] = trim($abbr_desc);
		}
	}

	function teardown() {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Clearing Extra-specific variables.
	#
		$this->footnotes = array();
		$this->footnotes_ordered = array();
		$this->abbr_desciptions = array();
		$this->abbr_word_re = '';

		parent::teardown();
	}


	### HTML Block Parser ###

	# Tags that are always treated as block tags:
	var $block_tags_re = 'p|div|h[1-6]|blockquote|pre|table|dl|ol|ul|address|form|fieldset|iframe|hr|legend';

The visibility should be declared for property $block_tags_re.

	# Tags treated as block tags only if the opening tag is alone on it's line:
	var $context_block_tags_re = 'script|noscript|math|ins|del';

The visibility should be declared for property $context_block_tags_re.

	# Tags where markdown="1" default to span mode:
	var $contain_span_tags_re = 'p|h[1-6]|li|dd|dt|td|th|legend|address';

The visibility should be declared for property $contain_span_tags_re.

	# Tags which must not have their contents modified, no matter where
	# they appear:
	var $clean_tags_re = 'script|math';

The visibility should be declared for property $clean_tags_re.

	# Tags that do not need to be closed.
	var $auto_close_tags_re = 'hr|img';

The visibility should be declared for property $auto_close_tags_re.

	function hashHTMLBlocks($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Hashify HTML Blocks and "clean tags".
	#
	# We only want to do this for block-level HTML tags, such as headers,
	# lists, and tables. That's because we still want to wrap <p>s around
	# "paragraphs" that are wrapped in non-block-level tags, such as anchors,
	# phrase emphasis, and spans. The list of tags we're looking for is
	# hard-coded.
	#
	# This works by calling _HashHTMLBlocks_InMarkdown, which then calls
	# _HashHTMLBlocks_InHTML when it encounter block tags. When the markdown="1"
	# attribute is found whitin a tag, _HashHTMLBlocks_InHTML calls back
	#  _HashHTMLBlocks_InMarkdown to handle the Markdown syntax within the tag.
	# These two functions are calling each other. It's recursive!
	#
		#
		# Call the HTML-in-Markdown hasher.
		#
		list($text, ) = $this->_hashHTMLBlocks_inMarkdown($text);

		return $text;
	}
	function _hashHTMLBlocks_inMarkdown($text, $indent = 0,

It is generally recommended to explicitly declare the visibility for methods.

										$enclosing_tag_re = '', $span = false)
	{
	#
	# Parse markdown text, calling _HashHTMLBlocks_InHTML for block tags.
	#
	# *   $indent is the number of space to be ignored when checking for code
	#     blocks. This is important because if we don't take the indent into
	#     account, something like this (which looks right) won't work as expected:
	#
	#     <div>
	#         <div markdown="1">
	#         Hello World.  <-- Is this a Markdown code block or text?
	#         </div>  <-- Is this a Markdown code block or a real tag?
	#     <div>
	#
	#     If you don't like this, just don't indent the tag on which
	#     you apply the markdown="1" attribute.
	#
	# *   If $enclosing_tag_re is not empty, stops at the first unmatched closing
	#     tag with that name. Nested tags supported.
	#
	# *   If $span is true, text inside must treated as span. So any double
	#     newline will be replaced by a single newline so that it does not create
	#     paragraphs.
	#
	# Returns an array of that form: ( processed text , remaining text )
	#
		if ($text === '') return array('', '');

		# Regex to check for the presense of newlines around a block tag.
		$newline_before_re = '/(?:^\n?|\n\n)*$/';
		$newline_after_re =
			'{
				^						# Start of text following the tag.
				(?>[ ]*<!--.*?-->)?		# Optional comment.
				[ ]*\n					# Must be followed by newline.
			}xs';

		# Regex to match any tag.
		$block_tag_re =
			'{
				(					# $2: Capture hole tag.
					</?					# Any opening or closing tag.
						(?>				# Tag name.
							'.$this->block_tags_re.'			|
							'.$this->context_block_tags_re.'	|
							'.$this->clean_tags_re.'        	|
							(?!\s)'.$enclosing_tag_re.'
						)
						(?:
							(?=[\s"\'/a-zA-Z0-9])	# Allowed characters after tag name.
							(?>
								".*?"		|	# Double quotes (can contain `>`)
								\'.*?\'   	|	# Single quotes (can contain `>`)
								.+?				# Anything but quotes and `>`.
							)*?
						)?
					>					# End of tag.
				|
					<!--    .*?     -->	# HTML Comment
				|
					<\?.*?\?> | <%.*?%>	# Processing instruction
				|
					<!\[CDATA\[.*?\]\]>	# CData Block
				|
					# Code span marker
					`+
				'. ( !$span ? ' # If not in span.
				|
					# Indented code block
					(?: ^[ ]*\n | ^ | \n[ ]*\n )
					[ ]{'.($indent+4).'}[^\n]* \n
					(?>
						(?: [ ]{'.($indent+4).'}[^\n]* | [ ]* ) \n
					)*
				|
					# Fenced code block marker
					(?> ^ | \n )
					[ ]{0,'.($indent).'}~~~+[ ]*\n
				' : '' ). ' # End (if not is span).
				)
			}xs';


		$depth = 0;		# Current depth inside the tag tree.
		$parsed = "";	# Parsed text that will be returned.

		#
		# Loop through every tag until we find the closing tag of the parent
		# or loop until reaching the end of text if no parent tag specified.
		#
		do {
			#
			# Split the text using the first $tag_match pattern found.
			# Text before  pattern will be first in the array, text after
			# pattern will be at the end, and between will be any catches made
			# by the pattern.
			#
			$parts = preg_split($block_tag_re, $text, 2,
								PREG_SPLIT_DELIM_CAPTURE);

			# If in Markdown span mode, add a empty-string span-level hash
			# after each newline to prevent triggering any block element.
			if ($span) {
				$void = $this->hashPart("", ':');
				$newline = "$void\n";
				$parts[0] = $void . str_replace("\n", $newline, $parts[0]) . $void;
			}

			$parsed .= $parts[0]; # Text before current tag.

			# If end of $text has been reached. Stop loop.
			if (count($parts) < 3) {
				$text = "";
				break;
			}

			$tag  = $parts[1]; # Tag to handle.
			$text = $parts[2]; # Remaining text after current tag.
			$tag_re = preg_quote($tag); # For use in a regular expression.

$tag_re is not used, you could remove the assignment.

			#
			# Check for: Code span marker
			#
			if ($tag{0} == "`") {
				# Find corresponding end marker.
				$tag_re = preg_quote($tag);
				if (preg_match('{^(?>.+?|\n(?!\n))*?(?<!`)'.$tag_re.'(?!`)}',

This code seems to be duplicated across your project.

					$text, $matches))
				{
					# End marker found: pass text unchanged until marker.
					$parsed .= $tag . $matches[0];
					$text = substr($text, strlen($matches[0]));
				}
				else {
					# Unmatched marker: just skip it.
					$parsed .= $tag;
				}
			}
			#
			# Check for: Fenced code block marker.
			#
			else if (preg_match('{^\n?[ ]{0,'.($indent+3).'}~}', $tag)) {
				# Fenced code block marker: find matching end marker.
				$tag_re = preg_quote(trim($tag));
				if (preg_match('{^(?>.*\n)+?[ ]{0,'.($indent).'}'.$tag_re.'[ ]*\n}', $text,

This code seems to be duplicated across your project.

					$matches))
				{
					# End marker found: pass text unchanged until marker.
					$parsed .= $tag . $matches[0];
					$text = substr($text, strlen($matches[0]));
				}
				else {
					# No end marker: just skip it.
					$parsed .= $tag;
				}
			}
			#
			# Check for: Indented code block.
			#
			else if ($tag{0} == "\n" || $tag{0} == " ") {
				# Indented code block: pass it unchanged, will be handled
				# later.
				$parsed .= $tag;
			}
			#
			# Check for: Opening Block level tag or
			#            Opening Context Block tag (like ins and del)
			#               used as a block tag (tag is alone on it's line).
			#
			else if (preg_match('{^<(?:'.$this->block_tags_re.')\b}', $tag) ||
				(	preg_match('{^<(?:'.$this->context_block_tags_re.')\b}', $tag) &&
					preg_match($newline_before_re, $parsed) &&
					preg_match($newline_after_re, $text)	)
				)
			{
				# Need to parse tag and following text using the HTML parser.
				list($block_text, $text) =
					$this->_hashHTMLBlocks_inHTML($tag . $text, "hashBlock", true);

				# Make sure it stays outside of any paragraph by adding newlines.
				$parsed .= "\n\n$block_text\n\n";
			}
			#
			# Check for: Clean tag (like script, math)
			#            HTML Comments, processing instructions.
			#
			else if (preg_match('{^<(?:'.$this->clean_tags_re.')\b}', $tag) ||
				$tag{1} == '!' || $tag{1} == '?')
			{
				# Need to parse tag and following text using the HTML parser.
				# (don't check for markdown attribute)
				list($block_text, $text) =
					$this->_hashHTMLBlocks_inHTML($tag . $text, "hashClean", false);

				$parsed .= $block_text;
			}
			#
			# Check for: Tag with same name as enclosing tag.
			#
			else if ($enclosing_tag_re !== '' &&
				# Same name as enclosing tag.
				preg_match('{^</?(?:'.$enclosing_tag_re.')\b}', $tag))
			{
				#
				# Increase/decrease nested tag count.
				#
				if ($tag{1} == '/')						$depth--;

This code seems to be duplicated across your project.

				else if ($tag{strlen($tag)-2} != '/')	$depth++;

				if ($depth < 0) {
					#
					# Going out of parent element. Clean up and break so we
					# return to the calling function.
					#
					$text = $tag . $text;
					break;
				}

				$parsed .= $tag;
			}
			else {
				$parsed .= $tag;
			}
		} while ($depth >= 0);

		return array($parsed, $text);
	}
	function _hashHTMLBlocks_inHTML($text, $hash_method, $md_attr) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Parse HTML, calling _HashHTMLBlocks_InMarkdown for block tags.
	#
	# *   Calls $hash_method to convert any blocks.
	# *   Stops when the first opening tag closes.
	# *   $md_attr indicate if the use of the `markdown="1"` attribute is allowed.
	#     (it is not inside clean tags)
	#
	# Returns an array of that form: ( processed text , remaining text )
	#
		if ($text === '') return array('', '');

		# Regex to match `markdown` attribute inside of a tag.
		$markdown_attr_re = '
			{
				\s*			# Eat whitespace before the `markdown` attribute
				markdown
				\s*=\s*
				(?>
					(["\'])		# $1: quote delimiter
					(.*?)		# $2: attribute value
					\1			# matching delimiter
				|
					([^\s>]*)	# $3: unquoted attribute value
				)
				()				# $4: make $3 always defined (avoid warnings)
			}xs';

		# Regex to match any tag.
		$tag_re = '{
				(					# $2: Capture hole tag.
					</?					# Any opening or closing tag.
						[\w:$]+			# Tag name.
						(?:
							(?=[\s"\'/a-zA-Z0-9])	# Allowed characters after tag name.
							(?>
								".*?"		|	# Double quotes (can contain `>`)
								\'.*?\'   	|	# Single quotes (can contain `>`)
								.+?				# Anything but quotes and `>`.
							)*?
						)?
					>					# End of tag.
				|
					<!--    .*?     -->	# HTML Comment
				|
					<\?.*?\?> | <%.*?%>	# Processing instruction
				|
					<!\[CDATA\[.*?\]\]>	# CData Block
				)
			}xs';

		$original_text = $text;		# Save original text in case of faliure.

		$depth		= 0;	# Current depth inside the tag tree.
		$block_text	= "";	# Temporary text holder for current text.
		$parsed		= "";	# Parsed text that will be returned.

		#
		# Get the name of the starting tag.
		# (This pattern makes $base_tag_name_re safe without quoting.)
		#
		if (preg_match('/^<([\w:$]*)\b/', $text, $matches))
			$base_tag_name_re = $matches[1];

		#
		# Loop through every tag until we find the corresponding closing tag.
		#
		do {
			#
			# Split the text using the first $tag_match pattern found.
			# Text before  pattern will be first in the array, text after
			# pattern will be at the end, and between will be any catches made
			# by the pattern.
			#
			$parts = preg_split($tag_re, $text, 2, PREG_SPLIT_DELIM_CAPTURE);

			if (count($parts) < 3) {
				#
				# End of $text reached with unbalenced tag(s).
				# In that case, we return original text unchanged and pass the
				# first character as filtered to prevent an infinite loop in the
				# parent function.
				#
				return array($original_text{0}, substr($original_text, 1));
			}

			$block_text .= $parts[0]; # Text before current tag.
			$tag         = $parts[1]; # Tag to handle.
			$text        = $parts[2]; # Remaining text after current tag.

			#
			# Check for: Auto-close tag (like <hr/>)
			#			 Comments and Processing Instructions.
			#
			if (preg_match('{^</?(?:'.$this->auto_close_tags_re.')\b}', $tag) ||
				$tag{1} == '!' || $tag{1} == '?')
			{
				# Just add the tag to the block as if it was text.
				$block_text .= $tag;
			}
			else {
				#
				# Increase/decrease nested tag count. Only do so if
				# the tag's name match base tag's.
				#
				if (preg_match('{^</?'.$base_tag_name_re.'\b}', $tag)) {

The variable $base_tag_name_re does not seem to be defined for all execution paths leading up to this point.

					if ($tag{1} == '/')						$depth--;

This code seems to be duplicated across your project.

					else if ($tag{strlen($tag)-2} != '/')	$depth++;
				}

				#
				# Check for `markdown="1"` attribute and handle it.
				#
				if ($md_attr &&
					preg_match($markdown_attr_re, $tag, $attr_m) &&
					preg_match('/^1|block|span$/', $attr_m[2] . $attr_m[3]))
				{
					# Remove `markdown` attribute from opening tag.
					$tag = preg_replace($markdown_attr_re, '', $tag);

					# Check if text inside this tag must be parsed in span mode.
					$this->mode = $attr_m[2] . $attr_m[3];

The property mode does not exist. Did you maybe forget to declare it?

					$span_mode = $this->mode == 'span' || $this->mode != 'block' &&
						preg_match('{^<(?:'.$this->contain_span_tags_re.')\b}', $tag);

					# Calculate indent before tag.
					if (preg_match('/(?:^|\n)( *?)(?! ).*?$/', $block_text, $matches)) {
						$strlen = $this->utf8_strlen;
						$indent = $strlen($matches[1], 'UTF-8');
					} else {
						$indent = 0;
					}

					# End preceding block with this tag.
					$block_text .= $tag;
					$parsed .= $this->$hash_method($block_text);

					# Get enclosing tag name for the ParseMarkdown function.
					# (This pattern makes $tag_name_re safe without quoting.)
					preg_match('/^<([\w:$]*)\b/', $tag, $matches);
					$tag_name_re = $matches[1];

					# Parse the content using the HTML-in-Markdown parser.
					list ($block_text, $text)
						= $this->_hashHTMLBlocks_inMarkdown($text, $indent,
							$tag_name_re, $span_mode);

					# Outdent markdown text.
					if ($indent > 0) {
						$block_text = preg_replace("/^[ ]{1,$indent}/m", "",
													$block_text);
					}

					# Append tag content to parsed text.
					if (!$span_mode)	$parsed .= "\n\n$block_text\n\n";
					else				$parsed .= "$block_text";

					# Start over a new block.
					$block_text = "";
				}
				else $block_text .= $tag;
			}

		} while ($depth > 0);

		#
		# Hash last block text that wasn't processed inside the loop.
		#
		$parsed .= $this->$hash_method($block_text);

		return array($parsed, $text);
	}


	function hashClean($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Called whenever a tag must be hashed when a function insert a "clean" tag
	# in $text, it pass through this function and is automaticaly escaped,
	# blocking invalid nested overlap.
	#
		return $this->hashPart($text, 'C');
	}


	function doHeaders($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Redefined to add id attribute support.
	#
		# Setext-style headers:
		#	  Header 1  {#header1}
		#	  ========
		#
		#	  Header 2  {#header2}
		#	  --------
		#
		$text = preg_replace_callback(
			'{
				(^.+?)								# $1: Header text
				(?:[ ]+\{\#([-_:a-zA-Z0-9]+)\})?	# $2: Id attribute
				[ ]*\n(=+|-+)[ ]*\n+				# $3: Header footer
			}mx',
			array(&$this, '_doHeaders_callback_setext'), $text);

		# atx-style headers:
		#	# Header 1        {#header1}
		#	## Header 2       {#header2}
		#	## Header 2 with closing hashes ##  {#header3}
		#	...
		#	###### Header 6   {#header2}
		#
		$text = preg_replace_callback('{
				^(\#{1,6})	# $1 = string of #\'s
				[ ]*
				(.+?)		# $2 = Header text
				[ ]*
				\#*			# optional closing #\'s (not counted)
				(?:[ ]+\{\#([-_:a-zA-Z0-9]+)\})? # id attribute
				[ ]*
				\n+
			}xm',
			array(&$this, '_doHeaders_callback_atx'), $text);

		return $text;
	}
	function _doHeaders_attr($attr) {

It is generally recommended to explicitly declare the visibility for methods.

		if (empty($attr))  return "";
		return " id=\"$attr\"";
	}
	function _doHeaders_callback_setext($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		if ($matches[3] == '-' && preg_match('{^- }', $matches[1]))

This code seems to be duplicated across your project.

			return $matches[0];
		$level = $matches[3]{0} == '=' ? 1 : 2;
		$attr  = $this->_doHeaders_attr($id =& $matches[2]);
		$block = "<h$level$attr>".$this->runSpanGamut($matches[1])."</h$level>";
		return "\n" . $this->hashBlock($block) . "\n\n";
	}
	function _doHeaders_callback_atx($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$level = strlen($matches[1]);
		$attr  = $this->_doHeaders_attr($id =& $matches[3]);
		$block = "<h$level$attr>".$this->runSpanGamut($matches[2])."</h$level>";
		return "\n" . $this->hashBlock($block) . "\n\n";
	}


	function doTables($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Form HTML tables.
	#
		$less_than_tab = $this->tab_width - 1;
		#
		# Find tables with leading pipe.
		#
		#	| Header 1 | Header 2
		#	| -------- | --------
		#	| Cell 1   | Cell 2
		#	| Cell 3   | Cell 4
		#
		$text = preg_replace_callback('
			{
				^							# Start of a line
				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				[|]							# Optional leading pipe (present)
				(.+) \n						# $1: Header row (at least one pipe)

				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				[|] ([ ]*[-:]+[-| :]*) \n	# $2: Header underline

				(							# $3: Cells
					(?>
						[ ]*				# Allowed whitespace.
						[|] .* \n			# Row content.
					)*
				)
				(?=\n|\Z)					# Stop at final double newline.
			}xm',
			array(&$this, '_doTable_leadingPipe_callback'), $text);

		#
		# Find tables without leading pipe.
		#
		#	Header 1 | Header 2
		#	-------- | --------
		#	Cell 1   | Cell 2
		#	Cell 3   | Cell 4
		#
		$text = preg_replace_callback('
			{
				^							# Start of a line
				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				(\S.*[|].*) \n				# $1: Header row (at least one pipe)

				[ ]{0,'.$less_than_tab.'}	# Allowed whitespace.
				([-:]+[ ]*[|][-| :]*) \n	# $2: Header underline

				(							# $3: Cells
					(?>
						.* [|] .* \n		# Row content
					)*
				)
				(?=\n|\Z)					# Stop at final double newline.
			}xm',
			array(&$this, '_DoTable_callback'), $text);

		return $text;
	}
	function _doTable_leadingPipe_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$head		= $matches[1];
		$underline	= $matches[2];
		$content	= $matches[3];

		# Remove leading pipe for each row.
		$content	= preg_replace('/^ *[|]/m', '', $content);

		return $this->_doTable_callback(array($matches[0], $head, $underline, $content));
	}
	function _doTable_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$head		= $matches[1];
		$underline	= $matches[2];
		$content	= $matches[3];

		# Remove any tailing pipes for each line.
		$head		= preg_replace('/[|] *$/m', '', $head);
		$underline	= preg_replace('/[|] *$/m', '', $underline);
		$content	= preg_replace('/[|] *$/m', '', $content);

		# Reading alignement from header underline.
		$separators	= preg_split('/ *[|] */', $underline);
		foreach ($separators as $n => $s) {
			if (preg_match('/^ *-+: *$/', $s))		$attr[$n] = ' align="right"';

$attr was never initialized. Although not strictly required by PHP, it is generally a good practice to add $attr = array(); before regardless.

			else if (preg_match('/^ *:-+: *$/', $s))$attr[$n] = ' align="center"';

The variable $attr does not seem to be defined for all execution paths leading up to this point.

			else if (preg_match('/^ *:-+ *$/', $s))	$attr[$n] = ' align="left"';
			else									$attr[$n] = '';
		}

		# Parsing span elements, including code spans, character escapes,
		# and inline HTML tags, so that pipes inside those gets ignored.
		$head		= $this->parseSpan($head);
		$headers	= preg_split('/ *[|] */', $head);
		$col_count	= count($headers);

		# Write column headers.
		$text = "<table>\n";
		$text .= "<thead>\n";
		$text .= "<tr>\n";
		foreach ($headers as $n => $header)
			$text .= "  <th$attr[$n]>".$this->runSpanGamut(trim($header))."</th>\n";
		$text .= "</tr>\n";
		$text .= "</thead>\n";

		# Split content by row.
		$rows = explode("\n", trim($content, "\n"));

		$text .= "<tbody>\n";
		foreach ($rows as $row) {
			# Parsing span elements, including code spans, character escapes,
			# and inline HTML tags, so that pipes inside those gets ignored.
			$row = $this->parseSpan($row);

			# Split row by cell.
			$row_cells = preg_split('/ *[|] */', $row, $col_count);
			$row_cells = array_pad($row_cells, $col_count, '');

			$text .= "<tr>\n";
			foreach ($row_cells as $n => $cell)
				$text .= "  <td$attr[$n]>".$this->runSpanGamut(trim($cell))."</td>\n";
			$text .= "</tr>\n";
		}
		$text .= "</tbody>\n";
		$text .= "</table>";

		return $this->hashBlock($text) . "\n";
	}


	function doDefLists($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Form HTML definition lists.
	#
		$less_than_tab = $this->tab_width - 1;

		# Re-usable pattern to match any entire dl list:
		$whole_list_re = '(?>
			(								# $1 = whole list
			  (								# $2
				[ ]{0,'.$less_than_tab.'}
				((?>.*\S.*\n)+)				# $3 = defined term
				\n?
				[ ]{0,'.$less_than_tab.'}:[ ]+ # colon starting definition
			  )
			  (?s:.+?)
			  (								# $4
				  \z
				|
				  \n{2,}
				  (?=\S)
				  (?!						# Negative lookahead for another term
					[ ]{0,'.$less_than_tab.'}
					(?: \S.*\n )+?			# defined term
					\n?
					[ ]{0,'.$less_than_tab.'}:[ ]+ # colon starting definition
				  )
				  (?!						# Negative lookahead for another definition
					[ ]{0,'.$less_than_tab.'}:[ ]+ # colon starting definition
				  )
			  )
			)
		)'; // mx

		$text = preg_replace_callback('{
				(?>\A\n?|(?<=\n\n))
				'.$whole_list_re.'
			}mx',
			array(&$this, '_doDefLists_callback'), $text);

		return $text;
	}
	function _doDefLists_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		# Re-usable patterns to match list item bullets and number markers:
		$list = $matches[1];

		# Turn double returns into triple returns, so that we can make a
		# paragraph for the last item in a list, if necessary:
		$result = trim($this->processDefListItems($list));
		$result = "<dl>\n" . $result . "\n</dl>";
		return $this->hashBlock($result) . "\n\n";
	}


	function processDefListItems($list_str) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Process the contents of a single definition list, splitting it
	#	into individual term and definition list items.
	#
		$less_than_tab = $this->tab_width - 1;

		# trim trailing blank lines:
		$list_str = preg_replace("/\n{2,}\\z/", "\n", $list_str);

		# Process definition terms.
		$list_str = preg_replace_callback('{
			(?>\A\n?|\n\n+)					# leading line
			(								# definition terms = $1
				[ ]{0,'.$less_than_tab.'}	# leading whitespace
				(?![:][ ]|[ ])				# negative lookahead for a definition
											#   mark (colon) or more whitespace.
				(?> \S.* \n)+?				# actual term (not whitespace).
			)
			(?=\n?[ ]{0,3}:[ ])				# lookahead for following line feed
											#   with a definition mark.
			}xm',
			array(&$this, '_processDefListItems_callback_dt'), $list_str);

		# Process actual definitions.
		$list_str = preg_replace_callback('{
			\n(\n+)?						# leading line = $1
			(								# marker space = $2
				[ ]{0,'.$less_than_tab.'}	# whitespace before colon
				[:][ ]+						# definition mark (colon)
			)
			((?s:.+?))						# definition text = $3
			(?= \n+ 						# stop at next definition mark,
				(?:							# next term or end of text
					[ ]{0,'.$less_than_tab.'} [:][ ]	|
					<dt> | \z
				)
			)
			}xm',
			array(&$this, '_processDefListItems_callback_dd'), $list_str);

		return $list_str;
	}
	function _processDefListItems_callback_dt($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$terms = explode("\n", trim($matches[1]));
		$text = '';
		foreach ($terms as $term) {
			$term = $this->runSpanGamut(trim($term));
			$text .= "\n<dt>" . $term . "</dt>";
		}
		return $text . "\n";
	}
	function _processDefListItems_callback_dd($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$leading_line	= $matches[1];
		$marker_space	= $matches[2];
		$def			= $matches[3];

		if ($leading_line || preg_match('/\n{2,}/', $def)) {

This code seems to be duplicated across your project.

			# Replace marker with the appropriate whitespace indentation
			$def = str_repeat(' ', strlen($marker_space)) . $def;
			$def = $this->runBlockGamut($this->outdent($def . "\n\n"));
			$def = "\n". $def ."\n";
		}
		else {
			$def = rtrim($def);
			$def = $this->runSpanGamut($this->outdent($def));
		}

		return "\n<dd>" . $def . "</dd>\n";
	}

	/**
	 * Adding the fenced code block syntax to regular Markdown:
	 *
	 * ~~~
	 * Code block
	 * ~~~
	 *
	 * ```php
	 * <?php echo "php!"
	 * ```
	 *
	 * @param string $text
	 */
	protected function doFencedCodeBlocks($text)
	{
		$less_than_tab = $this->tab_width;

$less_than_tab is not used, you could remove the assignment.

		$text = preg_replace_callback('{
				(?:\n|\A)
				# 1: Opening marker
				(
					[~`]{3,} # Marker: three tilde or more. // @olvlv: ~ or `
				)
				(\S*)[ ]* \n # Whitespace and newline following marker. // @olvlv code block type

				# 2: Content
				(
					(?>
						(?!\1 [ ]* \n)	# Not a closing marker.
						.*\n+
					)+
				)

				# Closing marker.
				\1 [ ]* \n
			}xm',
			array($this, '_doFencedCodeBlocks_callback'), $text);

		return $text;
	}

	protected function _doFencedCodeBlocks_callback($matches) // @olvlv update to support "type"
	{
		$class = $matches[2];
		$codeblock = $matches[3];

		if ($class)
		{
			$codeblock = $this->format_codeblock($codeblock, $class);

It seems like you code against a specific sub-type and not the parent class MarkdownExtra_Parser as the method format_codeblock() does only exist in the following sub-classes of MarkdownExtra_Parser: Textmark_Parser. Maybe you want to instanceof check for one of these explicitly?

			$codeblock = $this->unhash($codeblock);
		}
		else
		{
			$codeblock = htmlspecialchars($codeblock, ENT_NOQUOTES);
			$codeblock = preg_replace_callback('/^\n+/', array($this, '_doFencedCodeBlocks_newlines'), $codeblock);
		}

		$codeblock = '<pre' . ($class ? ' class="' . $class . '"' : '') . '><code>' . $codeblock . '</code></pre>';

		return "\n\n".$this->hashBlock($codeblock)."\n\n";
	}

	function _doFencedCodeBlocks_newlines($matches)

It is generally recommended to explicitly declare the visibility for methods.

	{
		return str_repeat("<br$this->empty_element_suffix", strlen($matches[0]));
	}


	#
	# Redefining emphasis markers so that emphasis by underscore does not
	# work in the middle of a word.
	#
	var $em_relist = array(

The visibility should be declared for property $em_relist.

		''  => '(?:(?<!\*)\*(?!\*)|(?<![a-zA-Z0-9_])_(?!_))(?=\S|$)(?![\.,:;]\s)',
		'*' => '(?<=\S|^)(?<!\*)\*(?!\*)',
		'_' => '(?<=\S|^)(?<!_)_(?![a-zA-Z0-9_])',
		);
	var $strong_relist = array(

The visibility should be declared for property $strong_relist.

		''   => '(?:(?<!\*)\*\*(?!\*)|(?<![a-zA-Z0-9_])__(?!_))(?=\S|$)(?![\.,:;]\s)',
		'**' => '(?<=\S|^)(?<!\*)\*\*(?!\*)',
		'__' => '(?<=\S|^)(?<!_)__(?![a-zA-Z0-9_])',
		);
	var $em_strong_relist = array(

The visibility should be declared for property $em_strong_relist.

		''    => '(?:(?<!\*)\*\*\*(?!\*)|(?<![a-zA-Z0-9_])___(?!_))(?=\S|$)(?![\.,:;]\s)',
		'***' => '(?<=\S|^)(?<!\*)\*\*\*(?!\*)',
		'___' => '(?<=\S|^)(?<!_)___(?![a-zA-Z0-9_])',
		);


	function formParagraphs($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	#	Params:
	#		$text - string to process with html <p> tags
	#
		# Strip leading and trailing lines:
		$text = preg_replace('/\A\n+|\n+\z/', '', $text);

		$grafs = preg_split('/\n{2,}/', $text, -1, PREG_SPLIT_NO_EMPTY);

		#
		# Wrap <p> tags and unhashify HTML blocks
		#
		foreach ($grafs as $key => $value) {
			$value = trim($this->runSpanGamut($value));

			# Check if this should be enclosed in a paragraph.
			# Clean tag hashes & block tag hashes are left alone.
			$is_p = !preg_match('/^B\x1A[0-9]+B|^C\x1A[0-9]+C$/', $value);

			if ($is_p) {
				$value = "<p>$value</p>";
			}
			$grafs[$key] = $value;
		}

		# Join grafs in one text, then unhash HTML tags.
		$text = implode("\n\n", $grafs);

		# Finish by removing any tag hashes still present in $text.
		$text = $this->unhash($text);

		return $text;
	}


	### Footnotes

	function stripFootnotes($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Strips link definitions from text, stores the URLs and titles in
	# hash references.
	#
		$less_than_tab = $this->tab_width - 1;

		# Link defs are in the form: [^id]: url "optional title"
		$text = preg_replace_callback('{
			^[ ]{0,'.$less_than_tab.'}\[\^(.+?)\][ ]?:	# note_id = $1
			  [ ]*
			  \n?					# maybe *one* newline
			(						# text = $2 (no blank lines allowed)
				(?:
					.+				# actual text
				|
					\n				# newlines but
					(?!\[\^.+?\]:\s)# negative lookahead for footnote marker.
					(?!\n+[ ]{0,3}\S)# ensure line is not blank and followed
									# by non-indented content
				)*
			)
			}xm',
			array(&$this, '_stripFootnotes_callback'),
			$text);
		return $text;
	}
	function _stripFootnotes_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$note_id = $this->fn_id_prefix . $matches[1];
		$this->footnotes[$note_id] = $this->outdent($matches[2]);
		return ''; # String that will replace the block
	}


	function doFootnotes($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Replace footnote references in $text [^id] with a special text-token
	# which will be replaced by the actual footnote marker in appendFootnotes.
	#
		if (!$this->in_anchor) {
			$text = preg_replace('{\[\^(.+?)\]}', "F\x1Afn:\\1\x1A:", $text);
		}
		return $text;
	}


	function appendFootnotes($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Append footnote list to text.
	#
		$text = preg_replace_callback('{F\x1Afn:(.*?)\x1A:}',
			array(&$this, '_appendFootnotes_callback'), $text);

		if (!empty($this->footnotes_ordered)) {
			$text .= "\n\n";
			$text .= "<div class=\"footnotes\">\n";
			$text .= "<hr". $this->empty_element_suffix ."\n";
			$text .= "<ol>\n\n";

			$attr = " rev=\"footnote\"";
			if ($this->fn_backlink_class != "") {
				$class = $this->fn_backlink_class;
				$class = $this->encodeAttribute($class);
				$attr .= " class=\"$class\"";
			}
			if ($this->fn_backlink_title != "") {
				$title = $this->fn_backlink_title;
				$title = $this->encodeAttribute($title);
				$attr .= " title=\"$title\"";
			}
			$num = 0;

			while (!empty($this->footnotes_ordered)) {
				$footnote = reset($this->footnotes_ordered);
				$note_id = key($this->footnotes_ordered);
				unset($this->footnotes_ordered[$note_id]);

				$footnote .= "\n"; # Need to append newline before parsing.
				$footnote = $this->runBlockGamut("$footnote\n");
				$footnote = preg_replace_callback('{F\x1Afn:(.*?)\x1A:}',
					array(&$this, '_appendFootnotes_callback'), $footnote);

				$attr = str_replace("%%", ++$num, $attr);
				$note_id = $this->encodeAttribute($note_id);

				# Add backlink to last paragraph; create new paragraph if needed.
				$backlink = "<a href=\"#fnref:$note_id\"$attr>&#8617;</a>";
				if (preg_match('{</p>$}', $footnote)) {
					$footnote = substr($footnote, 0, -4) . "&#160;$backlink</p>";
				} else {
					$footnote .= "\n\n<p>$backlink</p>";
				}

				$text .= "<li id=\"fn:$note_id\">\n";
				$text .= $footnote . "\n";
				$text .= "</li>\n\n";
			}

			$text .= "</ol>\n";
			$text .= "</div>";
		}
		return $text;
	}
	function _appendFootnotes_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$node_id = $this->fn_id_prefix . $matches[1];

		# Create footnote marker only if it has a corresponding footnote *and*
		# the footnote hasn't been used by another marker.
		if (isset($this->footnotes[$node_id])) {
			# Transfert footnote content to the ordered list.
			$this->footnotes_ordered[$node_id] = $this->footnotes[$node_id];
			unset($this->footnotes[$node_id]);

			$num = $this->footnote_counter++;
			$attr = " rel=\"footnote\"";
			if ($this->fn_link_class != "") {
				$class = $this->fn_link_class;
				$class = $this->encodeAttribute($class);
				$attr .= " class=\"$class\"";
			}
			if ($this->fn_link_title != "") {
				$title = $this->fn_link_title;
				$title = $this->encodeAttribute($title);
				$attr .= " title=\"$title\"";
			}

			$attr = str_replace("%%", $num, $attr);
			$node_id = $this->encodeAttribute($node_id);

			return
				"<sup id=\"fnref:$node_id\">".
				"<a href=\"#fn:$node_id\"$attr>$num</a>".
				"</sup>";
		}

		return "[^".$matches[1]."]";
	}


	### Abbreviations ###

	function stripAbbreviations($text) {

It is generally recommended to explicitly declare the visibility for methods.

This method seems to be duplicated in your project.

	#
	# Strips abbreviations from text, stores titles in hash references.
	#
		$less_than_tab = $this->tab_width - 1;

		# Link defs are in the form: [id]*: url "optional title"
		$text = preg_replace_callback('{
			^[ ]{0,'.$less_than_tab.'}\*\[(.+?)\][ ]?:	# abbr_id = $1
			(.*)					# text = $2 (no blank lines allowed)
			}xm',
			array(&$this, '_stripAbbreviations_callback'),
			$text);
		return $text;
	}
	function _stripAbbreviations_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$abbr_word = $matches[1];
		$abbr_desc = $matches[2];
		if ($this->abbr_word_re)
			$this->abbr_word_re .= '|';
		$this->abbr_word_re .= preg_quote($abbr_word);
		$this->abbr_desciptions[$abbr_word] = trim($abbr_desc);
		return ''; # String that will replace the block
	}


	function doAbbreviations($text) {

It is generally recommended to explicitly declare the visibility for methods.

	#
	# Find defined abbreviations in text and wrap them in <abbr> elements.
	#
		if ($this->abbr_word_re) {
			// cannot use the /x modifier because abbr_word_re may
			// contain significant spaces:
			$text = preg_replace_callback('{'.
				'(?<![\w\x1A])'.
				'(?:'.$this->abbr_word_re.')'.
				'(?![\w\x1A])'.
				'}',
				array(&$this, '_doAbbreviations_callback'), $text);
		}
		return $text;
	}
	function _doAbbreviations_callback($matches) {

It is generally recommended to explicitly declare the visibility for methods.

		$abbr = $matches[0];
		if (isset($this->abbr_desciptions[$abbr])) {
			$desc = $this->abbr_desciptions[$abbr];
			if (empty($desc)) {
				return $this->hashPart("<abbr>$abbr</abbr>");
			} else {
				$desc = $this->encodeAttribute($desc);
				return $this->hashPart("<abbr title=\"$desc\">$abbr</abbr>");
			}
		} else {
			return $matches[0];
		}
	}

}


/*

PHP Markdown Extra
==================

Description
-----------

This is a PHP port of the original Markdown formatter written in Perl
by John Gruber. This special "Extra" version of PHP Markdown features
further enhancements to the syntax for making additional constructs
such as tables and definition list.

Markdown is a text-to-HTML filter; it translates an easy-to-read /
easy-to-write structured text format into HTML. Markdown's text format
is most similar to that of plain text email, and supports features such
as headers, *emphasis*, code blocks, blockquotes, and links.

Markdown's syntax is designed not as a generic markup language, but
specifically to serve as a front-end to (X)HTML. You can use span-level
HTML tags anywhere in a Markdown document, and you can use block level
HTML tags (like <div> and <table> as well).

For more information about Markdown's syntax, see:

<http://daringfireball.net/projects/markdown/>


Bugs
----

To file bug reports please send email to:

<michel.fortin@michelf.com>

Please include with your report: (1) the example input; (2) the output you
expected; (3) the output Markdown actually produced.


Version History
---------------

See the readme file for detailed release notes for this version.


Copyright and License
---------------------

PHP Markdown & Extra
Copyright (c) 2004-2009 Michel Fortin
<http://michelf.com/>
All rights reserved.

Based on Markdown
Copyright (c) 2003-2006 John Gruber
<http://daringfireball.net/>
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

*	Redistributions of source code must retain the above copyright notice,
	this list of conditions and the following disclaimer.

*	Redistributions in binary form must reproduce the above copyright
	notice, this list of conditions and the following disclaimer in the
	documentation and/or other materials provided with the distribution.

*	Neither the name "Markdown" nor the names of its contributors may
	be used to endorse or promote products derived from this software
	without specific prior written permission.

This software is provided by the copyright holders and contributors "as
is" and any express or implied warranties, including, but not limited
to, the implied warranties of merchantability and fitness for a
particular purpose are disclaimed. In no event shall the copyright owner
or contributors be liable for any direct, indirect, incidental, special,
exemplary, or consequential damages (including, but not limited to,
procurement of substitute goods or services; loss of use, data, or
profits; or business interruption) however caused and on any theory of
liability, whether in contract, strict liability, or tort (including
negligence or otherwise) arising in any way out of the use of this
software, even if advised of the possibility of such damage.

*/