This is my function.php

function.php

<?php


/*----------------------- Remowe admin bar --------------------------*/

	show_admin_bar( false );
	
/*----------------------- Include shortcodes --------------------------*/

	add_filter('the_content', 'do_shortcode');
	include("shortcodes.php");
	
/*----------------------- Include widgets --------------------------*/
//	$temppath = get_template_directory_uri();
//	include('/widgets/kontakty.php');
	
/*----------------------- Add rel="prettyphoto"  --------------------------*/
	add_filter('the_content', 'addlightboxrel_replace');
	function addlightboxrel_replace ($content)
{	global $post;
	$pattern = "/<a(.*?)href=('|\")(.*?).(bmp|gif|jpeg|jpg|png)('|\")(.*?)>/i";
  	$replacement = '<a$1href=$2$3.$4$5 class="prettyPhoto" rel="prettyPhoto"$6>';
    $content = preg_replace($pattern, $replacement, $content);
	$content = str_replace("%LIGHTID%", $post->ID, $content);
    return $content;
}

	
/*----------------------- Disabling Wordpress wpautop and wptexturize filters. --------------------------*/
	
	function webtreats_formatter($content) {
	$new_content = '';

	/* Matches the contents and the open and closing tags */
	$pattern_full = '{(\[raw\].*?\[/raw\])}is';

	/* Matches just the contents */
	$pattern_contents = '{\[raw\](.*?)\[/raw\]}is';

	/* Divide content into pieces */
	$pieces = preg_split($pattern_full, $content, -1, PREG_SPLIT_DELIM_CAPTURE);

	/* Loop over pieces */
	foreach ($pieces as $piece) {
		/* Look for presence of the shortcode */
		if (preg_match($pattern_contents, $piece, $matches)) {

			/* Append to content (no formatting) */
			$new_content .= $matches[1];
		} else {

			/* Format and append to content */
			$new_content .= wptexturize(wpautop($piece));
		}
	}

	return $new_content;
}

// Remove the 2 main auto-formatters
remove_filter('the_content', 'wpautop');
remove_filter('the_content', 'wptexturize');

// Before displaying for viewing, apply this function
add_filter('the_content', 'webtreats_formatter', 99);
add_filter('widget_text', 'webtreats_formatter', 99);


/*----------------------- Sidebary --------------------------*/

//Page sidebar
	if ( function_exists('register_sidebar') )  
		register_sidebar(array(  
		'name' => 'Page sidebar',  
		'before_widget' => '<div id="widget_box">',  
		'after_widget' => '</div>',  
		'before_title' => '<h3 id="widget-title">',  
		'after_title' => '</h3>',  
	));

//Blog sidebar
	if ( function_exists('register_sidebar') )  
		register_sidebar(array(  
		'name' => 'Blog sidebar',  
		'before_widget' => '<div id="widget_box">',  
		'after_widget' => '</div>',  
		'before_title' => '<h3 id="widget-title">',  
		'after_title' => '</h3>',  
	));

	
  //Single post sidebar
  if ( function_exists('register_sidebar') )  
	  register_sidebar(array(  
	  'name' => 'Post sidebar',  
	  'before_widget' => '<div id="widget_box">',  
	  'after_widget' => '</div>',  
	  'before_title' => '<h3 id="widget-title">',  
	  'after_title' => '</h3>',  
  ));

	
/*----------------------- Footer sidebars --------------------------*/

//Footer sidebar 1 
if ( function_exists('register_sidebar') )  
    register_sidebar(array(  
    'name' => 'Footer sidebar 1',  
    'before_widget' => '<div id="widget_box">',  
    'after_widget' => '</div>',  
    'before_title' => '<h3 id="widget-title">',  
    'after_title' => '</h3>',  
)); 


//Footer sidebar 2 
if ( function_exists('register_sidebar') )  
    register_sidebar(array(  
    'name' => 'Footer sidebar 2',  
    'before_widget' => '<div id="widget_box">',  
    'after_widget' => '</div>',  
    'before_title' => '<h3 id="widget-title">',  
    'after_title' => '</h3>',  
)); 

//Footer sidebar 3 
if ( function_exists('register_sidebar') )  
    register_sidebar(array(  
    'name' => 'Footer sidebar 3',  
    'before_widget' => '<div id="widget_box">',  
    'after_widget' => '</div>',  
    'before_title' => '<h3 id="widget-title">',  
    'after_title' => '</h3>',  
)); 

//Footer sidebar 4 
if ( function_exists('register_sidebar') )  
    register_sidebar(array(  
    'name' => 'Footer sidebar 4',  
    'before_widget' => '<div id="widget_box">',  
    'after_widget' => '</div>',  
    'before_title' => '<h3 id="widget-title">',  
    'after_title' => '</h3>',  
)); 	


/*----------------------- Registrování menu --------------------------*/

register_nav_menu( 'primary', 'Hlavní menu' ); 

$defaults = array(
  'theme_location'  => '',
  'menu'            => '', 
  'container'       => 'div', 
  'container_class' => 'menu-{menu slug}-container', 
  'container_id'    => '',
  'menu_class'      => 'menu', 
  'menu_id'         => '',
  'echo'            => true,
  'fallback_cb'     => 'wp_page_menu',
  'before'          => '',
  'after'           => '',
  'link_before'     => '',
  'link_after'      => '',
  'items_wrap'      => '<ul id=\"%1$s\" class=\"%2$s\">%3$s</ul>',
  'depth'           => 0,
  'walker'          => '');
  
/*--------------------- Register all scripts ------------------------*/

		function register_js() {
		if (!is_admin()) {
			wp_deregister_script('jquery');
			wp_register_script('jquery', 'http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js');
			wp_register_script('quicksand', get_template_directory_uri() . '/js/jquery.quicksand.js', 'jquery');
			wp_register_script('easing', get_template_directory_uri() . '/js/jquery.easing.1.3.js', 'jquery');
			wp_register_script('custom', get_template_directory_uri() . '/js/jquery.custom.js', 'jquery', '1.0', TRUE);
			wp_register_script('prettyPhoto', get_template_directory_uri() . '/js/jquery.prettyPhoto.js', 'jquery');
			wp_register_script('flexslider', get_bloginfo( 'template_directory' ) .'/js/jquery.flexslider.js' );
			wp_register_script('bootstrap', get_template_directory_uri() . '/js/bootstrap.js', 'jquery');
			wp_register_script('metaboxcustom', get_template_directory_uri() . '/js/custom-js.js', 'jquery', '1.0', TRUE);
			wp_register_script('jqueryuimin', get_template_directory_uri() . '/js/jquery-ui.min.js', 'jquery', '1.0', TRUE);
			wp_register_script('otherjs', get_template_directory_uri() . '/js/otherjs.js', 'jquery', '1.0', TRUE);
			
			
			wp_enqueue_script('jquery');
			wp_enqueue_script('quicksand');
			wp_enqueue_script('prettyPhoto');
			wp_enqueue_script('easing');
			wp_enqueue_script('custom');
			wp_enqueue_script('flexslider');
			wp_enqueue_script('bootstrap');
			wp_enqueue_script('metaboxcustom');
			wp_enqueue_script('jqueryuimin');
			wp_enqueue_script('otherjs');
		}
	}
	
	add_action('init', 'register_js');
	
/*--------------------- Register all styles ------------------------*/
	function register_styles()
	{
		if (!is_admin()) {
			wp_register_style('prettyPhoto', get_template_directory_uri() .	'/css/prettyPhoto.css');
			wp_register_style('bootstrap', get_template_directory_uri() .	'/css/bootstrap.css');
			wp_register_style('style', get_template_directory_uri() .	'/style.css');
			wp_register_style('flexslider', get_template_directory_uri() .	'/css/flexslider.css');
			
			wp_enqueue_style( 'prettyPhoto');
			wp_enqueue_style( 'bootstrap');
			wp_enqueue_style( 'style');
			wp_enqueue_style( 'flexslider');
		}		
	}
	
	add_action('init', 'register_styles');
	
	
/*--------------------- Vložení porfolio ------------------------*/

	// Include the portfolio functionality
	include("portfolio/portfolio-post-type.php");
	
	
/*--------------------- Post types ------------------------*/

// Hlavní články
add_action('init', 'hlavni_clanky_register');
 
function hlavni_clanky_register() {
 
	$labels = array(
		'name' => _x('Hlavní články', 'post type general name'),
		'singular_name' => _x('Hlavní článek', 'post type singular name'),
		'add_new' => _x('Přidat nový', 'portfolio item'),
		'add_new_item' => __('Přidat nový hlavní článek'),
		'edit_item' => __('Upravit hlavní článek'),
		'new_item' => __('Nový hlavní článek'),
		'view_item' => __('Zobrazit hlavní článek'),
		'search_items' => __('Hledat hlavní článek'),
		'not_found' =>  __('Nic nenalezeno'),
		'not_found_in_trash' => __('Nic nenalezeno v koši'),
		'parent_item_colon' => ''
	);
 
	$args = array(
		'labels' => $labels,
		'public' => true,
		'publicly_queryable' => true,
		'show_ui' => true,
		'query_var' => true,
	  //'menu_icon' => get_stylesheet_directory_uri() . '/article16.png',
		'rewrite' => true,
		'capability_type' => 'post',
		'hierarchical' => false,
		'menu_position' => 5,
		'supports' => array('title','editor','thumbnail')
	  ); 
 
	register_post_type( 'hlavni_clanky' , $args );
}

/*--------------------- Excerpt ------------------------*/

function my_excerpt($excerpt_length = 55, $id = false, $echo = true) {
         
    $text = '';
   
          if($id) {
                $the_post = & get_post( $my_id = $id );
                $text = ($the_post->post_excerpt) ? $the_post->post_excerpt : $the_post->post_content;
          } else {
                global $post;
                $text = ($post->post_excerpt) ? $post->post_excerpt : get_the_content('');
    }
         
                $text = strip_shortcodes( $text );
                $text = apply_filters('the_content', $text);
                $text = str_replace(']]>', ']]&gt;', $text);
          $text = strip_tags($text);
       
                $excerpt_more = ' ' . '...';
                $words = preg_split("/[\n\r\t ]+/", $text, $excerpt_length + 1, PREG_SPLIT_NO_EMPTY);
                if ( count($words) > $excerpt_length ) {
                        array_pop($words);
                        $text = implode(' ', $words);
                        $text = $text . $excerpt_more;
                } else {
                        $text = implode(' ', $words);
                }
        if($echo)
  echo apply_filters('the_content', $text);
        else
        return $text;
}
 
function get_my_excerpt($excerpt_length = 55, $id = false, $echo = false) {
 return my_excerpt($excerpt_length, $id, $echo);
}


/*--------------------- Metaboxes one ------------------------*/

include_once 'functions/add_meta_box.php';


/*--------------------- Thumbnail sizes ------------------------*/

if ( function_exists( 'add_theme_support' ) ) { // Added in 2.9
    add_theme_support( 'post-thumbnails' );
    add_image_size( 'homepage-thumbnail', 216, 116, true); // Homepage thumbnail size
    add_image_size( 'blog_fullwidth', 1158, 320, true); // Blog full width size
    add_image_size( 'blog_tree_column', 358, 170, true); // Blog tree columns size
    add_image_size( 'blog_sidebar', 696, 230, true); // Blog with sidebar size
    add_image_size( 'portfolio_one', 1158, 300, true); // Blog with sidebar size
    add_image_size( 'portfolio_two', 558, 196, true); // Blog with sidebar size
    add_image_size( 'portfolio_three', 358, 170, true); // Blog with sidebar size
    add_image_size( 'portfolio_four', 266, 140, true); // Blog with sidebar size
    add_image_size( 'recent_post', 50, 50, true); // Blog with sidebar size

}


// This was not meant not to replace your functions.php file. Just copy and paste the codes below into your own functions.php file.

/*-----------------------------------------------------------------------------------*/
// Options Framework
/*-----------------------------------------------------------------------------------*/

// Paths to admin functions
define('ADMIN_PATH', STYLESHEETPATH . '/admin/');
define('ADMIN_DIR', get_template_directory_uri() . '/admin/');
define('LAYOUT_PATH', ADMIN_PATH . '/layouts/');

// You can mess with these 2 if you wish.
$themedata = get_theme_data(STYLESHEETPATH . '/style.css');
define('THEMENAME', $themedata['Name']);
define('OPTIONS', 'of_options'); // Name of the database row where your options are stored
define('BACKUPS','of_backups'); // Name of the database row for options backup

// Build Options
require_once (ADMIN_PATH . 'admin-interface.php');		// Admin Interfaces 
require_once (ADMIN_PATH . 'theme-options.php'); 		// Options panel settings and custom settings
require_once (ADMIN_PATH . 'admin-functions.php'); 	// Theme actions based on options settings
require_once (ADMIN_PATH . 'medialibrary-uploader.php'); // Media Library Uploader