var presentation = ["<word>pliable structure<\/word>","<word>hydrophilic or water-loving<\/word>","<word>hydrophobic or water-fearing<\/word>","<word>amphipathic molecule<\/word>","<word>Intracellular fluid (ICF)<\/word>","<word>Extracellular fluid (ECF)<\/word>","<word>Interstitial fluid (IF)<\/word>","<word>integral proteins and peripheral protein<\/word>","<word>channel protein<\/word>","<word>recognition proteins<\/word>","<word>ligand<\/word>","<word>glycoprotein<\/word>","<word>glycocalyx is a fuzzy-appearing coating around the cell<\/word>","<word>person's genetic makeup<\/word>","<word>ability to regulate the concentration of substances inside the cell<\/word>","<word>selectively permeable<\/word>","<word>Passive transport<\/word>","<word>active transport<\/word>","<phrase>The cell membrane is an extremely <strong data-readahead=\"pliable structure\" class=\"presentation_word\">pliable structure<\/strong> composed primarily of back-to-back phospholipids (a \"bi-layer\"). Cholesterol is also present, which contributes to the fluidity of the membrane, and there are various proteins embedded within the membrane that have a variety of functions.\nA single phospholipid molecule has a phosphate group on one end, called the \"head,\" and two side-by-side chains of fatty acids that make up the lipid tails. The phosphate group is negatively charged, making the head polar and <strong data-readahead=\"hydrophilic or water-loving\" class=\"presentation_word\">hydrophilic or water-loving<\/strong>. A hydrophilic molecule (or region of a molecule) is one that is attracted to water. The phosphate heads are thus attracted to the water molecules of both the extracellular and intracellular environments. The lipid tails, on the other hand, are uncharged, or non-polar, and are <strong data-readahead=\"hydrophobic or water-fearing\" class=\"presentation_word\">hydrophobic or water-fearing<\/strong>. A hydrophobic molecule (or region of a molecule) repels and is repelled by water. Some lipid tails consist of saturated fatty acids and some contain unsaturated fatty acids. This combination adds to the fluidity of the tails that are constantly in motion. Phospholipids are thus amphipathic molecules. An <strong data-readahead=\"amphipathic molecule\" class=\"presentation_word\">amphipathic molecule<\/strong> is one that contains both a hydrophilic and a hydrophobic region. In fact, soap works to remove oil and grease stains because it has amphipathic properties. The hydrophilic portion can dissolve in water while the hydrophobic portion can trap grease in micelles that then can be washed away.\nThe cell membrane consists of two adjacent layers of phospholipids. The lipid tails of one layer face the lipid tails of the other layer, meeting at the interface of the two layers. The phospholipid heads face outward, one layer exposed to the interior of the cell and one layer exposed to the exterior. Because the phosphate groups are polar and hydrophilic, they are attracted to water in the intracellular fluid. <strong data-readahead=\"Intracellular fluid (ICF)\" class=\"presentation_word\">Intracellular fluid (ICF)<\/strong> is the fluid interior of the cell. The phosphate groups are also attracted to the extracellular fluid. <strong data-readahead=\"Extracellular fluid (ECF)\" class=\"presentation_word\">Extracellular fluid (ECF)<\/strong> is the fluid environment outside the enclosure of the cell membrane. <strong data-readahead=\"Interstitial fluid (IF)\" class=\"presentation_word\">Interstitial fluid (IF)<\/strong> is the term given to extracellular fluid not contained within blood vessels. Because the lipid tails are hydrophobic, they meet in the inner region of the membrane, excluding watery intracellular and extracellular fluid from this space. The cell membrane has many proteins, as well as other lipids (such as cholesterol), that are associated with the phospholipid bilayer. An important feature of the membrane is that it remains fluid; the lipids and proteins in the cell membrane are not rigidly locked in place.\nMembrane Proteins\nThe lipid bilayer forms the basis of the cell membrane, but it is peppered throughout with various proteins. Two different types of proteins that are commonly associated with the cell membrane are the <strong data-readahead=\"integral proteins and peripheral protein\" class=\"presentation_word\">integral proteins and peripheral protein<\/strong>. As its name suggests, an integral protein is a protein that is embedded in the membrane. A <strong data-readahead=\"channel protein\" class=\"presentation_word\">channel protein<\/strong> is an example of an integral protein that selectively allows particular materials, such as certain ions, to pass into or out of the cell.\nAnother important group of integral proteins are cell <strong data-readahead=\"recognition proteins\" class=\"presentation_word\">recognition proteins<\/strong>, which serve to mark a cell's identity so that it can be recognized by other cells. A receptor is a type of recognition protein that can selectively bind a specific molecule outside the cell, and this binding induces a chemical reaction within the cell. A <strong data-readahead=\"ligand\" class=\"presentation_word\">ligand<\/strong> is a specific molecule that binds to and activates a receptor. Some integral proteins serve dual roles as both a receptor and an ion channel. One example of a receptor-<strong data-readahead=\"ligand\">ligand<\/strong> interaction is the receptors on nerve cells that bind neurotransmitters, such as dopamine. When a dopamine molecule binds to a dopamine receptor protein, a channel within the transmembrane protein opens to allow certain ions to flow into the cell.\nSome integral membrane proteins are glycoproteins. A <strong data-readahead=\"glycoprotein\" class=\"presentation_word\">glycoprotein<\/strong> is a protein that has carbohydrate molecules attached, which extend into the extracellular matrix. The attached carbohydrate tags on glycoproteins aid in cell recognition. The carbohydrates that extend from membrane proteins and even from some membrane lipids collectively form the glycocalyx. The <strong data-readahead=\"glycocalyx is a fuzzy-appearing coating around the cell\" class=\"presentation_word\">glycocalyx is a fuzzy-appearing coating around the cell<\/strong> formed from glycoproteins and other carbohydrates attached to the cell membrane. The glycocalyx can have various roles. For example, it may have molecules that allow the cell to bind to another cell, it may contain receptors for hormones, or it might have enzymes to break down nutrients. The glycocalyces found in a person's body are products of that <strong data-readahead=\"person's genetic makeup\" class=\"presentation_word\">person's genetic makeup<\/strong>. They give each of the individual's trillions of cells the \"identity\" of belonging in the person's body. This identity is the primary way that a person's immune defense cells \"know\" not to attack the person's own body cells, but it also is the reason organs donated by another person might be rejected.\nPeripheral proteins are typically found on the inner or outer surface of the lipid bilayer but can also be attached to the internal or external surface of an integral protein. These proteins typically perform a specific function for the cell. Some peripheral proteins on the surface of intestinal cells, for example, act as digestive enzymes to break down nutrients to sizes that can pass through the cells and into the bloodstream.\nTransport across the Cell Membrane\nOne of the great wonders of the cell membrane is its <strong data-readahead=\"ability to regulate the concentration of substances inside the cell\" class=\"presentation_word\">ability to regulate the concentration of substances inside the cell<\/strong>. These substances include ions such as Ca++, Na+, K+, and Cl\u2013; nutrients including sugars, fatty acids, and amino acids; and waste products, particularly carbon dioxide (CO2), which must leave the cell.\nThe membrane's lipid bilayer structure provides the first level of control. The phospholipids are tightly packed together, and the membrane has a hydrophobic interior. This structure causes the membrane to be <strong data-readahead=\"selectively permeable\" class=\"presentation_word\">selectively permeable<\/strong>. A membrane that has selective permeability allows only substances meeting certain criteria to pass through it unaided. In the case of the cell membrane, only relatively small, nonpolar materials can move through the lipid bilayer (remember, the lipid tails of the membrane are nonpolar). Some examples of these are other lipids, oxygen and carbon dioxide gases, and alcohol. However, water-soluble materials-like glucose, amino acids, and electrolytes-need some assistance to cross the membrane because they are repelled by the hydrophobic tails of the phospholipid bilayer. All substances that move through the membrane do so by one of two general methods, which are categorized based on whether or not energy is required. <strong data-readahead=\"Passive transport\" class=\"presentation_word\">Passive transport<\/strong> is the movement of substances across the membrane without the expenditure of cellular energy. In contrast, <strong data-readahead=\"active transport\" class=\"presentation_word\">active transport<\/strong> is the movement of substances across the membrane using energy from adenosine triphosphate (ATP).<\/phrase>"];
	var currentPosition = 0;
	var totalPositions = 0;
	var timePerWord = 1500;
	var timePerPhraseWord = 120
	var readAheadPlayerTimer;
	var autoPlay = true;
	var setMinimized = false;

	var wordSpeedOptions = {'Slower':2000,'Moderate':1200,'Fast':800};
	var phraseSpeedOptions = {'Slower':280,'Moderate':200,'Fast':80};
	var defaultWordSpeedOption = 'Moderate';
	var defaultPhraseSpeedOption = 'Moderate';
	var logToLTI = false;

	$(window).load(function(){
		totalPositions = presentation.length;
		if (totalPositions > 0){
			$('body').prepend('<div id="read_ahead_player_back"></div>');
			$('body').prepend('<div id="read_ahead_player"></div>');
			$('#read_ahead_player').prepend('<div id="read_ahead_player_field" class="read_ahead_word_section"></div>');
			initializeReadAheadControls();
			initializeReadAheadSlider();
			initializeReadAheadSpeedOptions();
			currentReadAheadControls();
			resumeReadAheadPlayback();
		}
	});

	$(document).keyup(function(e){
		switch(e.which) {
			case 37: 
				pauseReadAheadPresentation();
				priorReadAheadPresentationItem();
				break;
			case 39:
				pauseReadAheadPresentation();
				nextReadAheadPresentationItem();
				break;
			default:
				break;
		}

	});

	function initializeReadAheadControls(){
		var s = '';
		s += '<a href="javascript:void(0)" onclick="read_ahead_switch_min_max(true);" id="read_ahead_player_max_min" class="player-icons" aria-label="minimize/maximize player">';
		s += '<span class="fa-stack fa-lg " aria-hidden><i class="fa fa-circle fa-stack-2x"></i><i class="fa fa-minus fa-stack-1x fa-inverse"></i></span>';
		s += '</a>';
		s += '<div id="read_ahead_controls">';
		s += '<a href="javascript:void(0)" onclick="priorReadAheadPresentationItem()" id="read_ahead_player_previous_word" class="player-icons" aria-label="previous keyword">';
		s += '<span class="fa-stack fa-lg " aria-hidden><i class="fa fa-circle fa-stack-2x"></i><i class="fa fa-backward fa-stack-1x fa-inverse"></i></span>';
		s += '</a>';
		s += '<a href="javascript:void(0)" onclick="pauseReadAheadPresentation()" id="read_ahead_player_pause_play" class="player-icons" aria-label="play/pause">';
		s += '<span class="fa-stack fa-lg " aria-hidden><i class="fa fa-circle fa-stack-2x"></i><i class="fa fa-pause fa-stack-1x fa-inverse"></i></span>';
		s += '</a>';
		s += '<a href="javascript:void(0)" onclick="nextReadAheadPresentationItem()" id="read_ahead_player_next_word" class="player-icons" aria-label="next keyword">';
		s += '<span class="fa-stack fa-lg " aria-hidden><i class="fa fa-circle fa-stack-2x"></i><i class="fa fa-forward fa-stack-1x fa-inverse"></i></span>';
		s += '</a>';
		s += '</div>';
		$('#read_ahead_player').append(s);
	}

	function initializeReadAheadSlider(){
		var s = '';
		s += '<div class="read_ahead_slider" id="readAheadSlider">';
		s += '<div class="read_ahead_slider_bar" id="readAheadSliderBar"></div>';
		s += '</div>';
		$('#read_ahead_controls').prepend(s);
		updateReadAheadSliderPosition();
	}

	function initializeReadAheadSpeedOptions(){
		var s = '<div id="read_ahead_player_options">';
		s += '<div class="slider_control" id="slider_control_word_speed">';
		s += ' Word Speed<br/>';
		s += '<div class="slider_bar">';
		optionCount = 0;
		for (index in wordSpeedOptions) { optionCount++; }
		optionWidth = 100 / optionCount;
		for (index in wordSpeedOptions) {
			var option = wordSpeedOptions[index];
			if (index == defaultWordSpeedOption) {
				s += '<a href="javascript:void(0)" id="slider_control_word_speed_'+option+'" onclick="updateReadAheadWordSpeed('+option+',this)" style="width:'+optionWidth+'%;" title="'+index+'" data-speed="'+option+'" class="current_speed" aria-label="'+index+'"></a>';
				updateReadAheadWordSpeed(option);
			} else {
				s += '<a href="javascript:void(0)" id="slider_control_word_speed_'+option+'" onclick="updateReadAheadWordSpeed('+option+',this)" style="width:'+optionWidth+'%;" title="'+index+'" data-speed="'+option+'" aria-label="'+index+'"></a>';
			}
		}
		s += '</div>';
		s += '</div>';
		s += '<div class="slider_control" id="slider_control_phrase_speed">';
		s += ' Phrase Speed<br/>';
		s += '<div class="slider_bar">';
		optionCount = 0;
		for (index in phraseSpeedOptions) { optionCount++; }
		optionWidth = 100 / optionCount;
		for (index in phraseSpeedOptions) {
			var option = phraseSpeedOptions[index];
			if (index == defaultWordSpeedOption) {
				s += '<a href="javascript:void(0)" id="slider_control_phrase_speed_'+option+'" onclick="updateReadAheadPhraseSpeed('+option+',this)" style="width:'+optionWidth+'%;" title="'+index+'" data-speed="'+option+'" class="current_speed" aria-label="'+index+'"></a>';
				updateReadAheadPhraseSpeed(option);
			} else {
				s += '<a href="javascript:void(0)" id="slider_control_phrase_speed_'+option+'" onclick="updateReadAheadPhraseSpeed('+option+',this)" style="width:'+optionWidth+'%;" title="'+index+'" data-speed="'+option+'" aria-label="'+index+'"></a>';
			}
		}
		s += '</div>';
		s += '</div>';
		s += '</div>';
		$('#read_ahead_controls').append(s);
	}

	function updateReadAheadWordSpeed(microseconds,sender) {
		microseconds = microseconds != undefined && microseconds > 0 ? microseconds : 0;
		if (microseconds > 0) { timePerWord = microseconds; }
		if (sender!=undefined) { 
			$('#slider_control_word_speed').find('a').removeClass('current_speed');
			$(sender).addClass('current_speed');
		}
		logReadAheadPlayerAction('updateReadAheadWordSpeed','Presentation',microseconds);
	}

	function updateReadAheadPhraseSpeed(microseconds,sender) {
		microseconds = microseconds != undefined && microseconds > 0 ? microseconds : 0;
		if (microseconds > 0 ) { timePerPhraseWord = microseconds; }
		if (sender!=undefined) { 
			$('#slider_control_phrase_speed').find('a').removeClass('current_speed');
			$(sender).addClass('current_speed');
		}
		logReadAheadPlayerAction('updateReadAheadPhraseSpeed','Presentation',microseconds);
	}

	function updateReadAheadSliderPosition(){
		var currentSliderBarWidth = 100 - (100 / totalPositions * (currentPosition + 1));
		$('#readAheadSliderBar').css('width',currentSliderBarWidth+'%');
	}

	function currentReadAheadControls(){
		$('#read_ahead_player_pause_play').show();
		if (currentPosition < totalPositions - 1)	{
			$('#read_ahead_player_next_word').removeClass('disabled');
		} else {
			$('#read_ahead_player_next_word').addClass('disabled');
		}
		if (currentPosition > 0) {
			$('#read_ahead_player_previous_word').removeClass('disabled');
		} else {
			$('#read_ahead_player_previous_word').addClass('disabled');
		}
	}

	function restartReadAheadPresentation(){
		currentPosition = 0;
		logReadAheadPlayerAction('restartReadAheadPresentation','Presentation','');
		resumeReadAheadPlayback();
	}

	function resumeReadAheadPlayback(){
		$('.fa-repeat').removeClass('fa-repeat').addClass('fa-play');
		$('#read_ahead_player_pause_play').each(function(){
			$(this).find('.fa-play').removeClass('fa-play').addClass('fa-pause');
			$(this).off('click');
			$(this).attr('onclick','pauseReadAheadPresentation()');
		});
		logReadAheadPlayerAction('resumeReadAheadPlayback','Presentation','');
		playReadAheadPresentation();
	}

	function pauseReadAheadPresentation(){
		$('#read_ahead_player_pause_play').each(function(){
			$(this).find('.fa-pause').removeClass('fa-pause').addClass('fa-play');
			$(this).off('click');
			$(this).attr('onclick','resumeReadAheadPlayback()');
		});
		logReadAheadPlayerAction('pauseReadAheadPresentation','Presentation','');
		read_ahead_pause();
	}

	function endReadAheadPresentation(){
		$('.fa-play').removeClass('fa-play').addClass('fa-repeat');
		$('.fa-pause').removeClass('fa-pause').addClass('fa-repeat');
		$('#read_ahead_player_pause_play').each(function(){
			$(this).off('click');
			$(this).attr('onclick','restartReadAheadPresentation()');
		});
		logReadAheadPlayerAction('endReadAheadPresentation','Presentation','');
		logLTIEndPresentation();
	}

	function playReadAheadPresentation(){
		autoPlay=true;
		currentPosition--;
		logReadAheadPlayerAction('playReadAheadPresentation','Presentation','');
		nextReadAheadPresentationItem(); 
	}

	function startReadAheadStepper(timeDisplayWord){
		clearInterval(readAheadPlayerTimer);
		readAheadPlayerTimer = setTimeout(function() { read_ahead_step(); },timeDisplayWord);
	}

	function stopReadAheadStepper(){
		clearInterval(readAheadPlayerTimer);
	}

	function read_ahead_step(){
		if (autoPlay) {
			nextReadAheadPresentationItem();
		}
	}

	function read_ahead_pause(){
		autoPlay=false;
		stopReadAheadStepper();
	}

	function showReadAheadPresentationItem(index){
		currentPosition = index;
		currentPresentationItem = presentation[currentPosition] != undefined ? presentation[currentPosition].trim() : "";
		if (currentPresentationItem != "") {
			currentItemWordCount = presentation[currentPosition].replace("\n","").split(" ").length;
			if (currentPresentationItem.startsWith("<word>")){
				startReadAheadStepper(currentItemWordCount*timePerWord);
				$('#read_ahead_player_field').html('<div class="read_ahead_word" style="display:block;">'+currentPresentationItem+'</div>');
				logReadAheadPlayerAction('showReadAheadPresentationItem','Word',currentPresentationItem);
		
			} else {
				startReadAheadStepper(currentItemWordCount*timePerPhraseWord);
				$('#read_ahead_player_field').html('<div class="read_ahead_text_box" style="display:block;"><div class="read_ahead_text">'+currentPresentationItem.replace("\n","<br />")+'</div></div>');
				logReadAheadPlayerAction('showReadAheadPresentationItem','Phrase','');
		
			}
		} else {
			if (currentPosition < totalPositions) {
				nextReadAheadPresentationItem();
			} else {
				endReadAheadPresentation();
				read_ahead_minimize();
			}
		}
		currentReadAheadControls();
		updateReadAheadSliderPosition();
		saveReadAheadPosition();
	}

	function priorReadAheadPresentationItem(){
		stopReadAheadStepper();
		logReadAheadPlayerAction('priorReadAheadPresentationItem','Controls','');
		showReadAheadPresentationItem(currentPosition-1);
	}


	function nextReadAheadPresentationItem(){
		stopReadAheadStepper();
		logReadAheadPlayerAction('nextReadAheadPresentationItem','Controls','');
		showReadAheadPresentationItem(currentPosition+1);
	}

	function read_ahead_playAgain(){
		currentWordIndex = 0;
		logReadAheadPlayerAction('read_ahead_playAgain','Controls','');
		playReadAheadPresentation();
	}


	function read_ahead_minimize(){
		setMinimized = true;
		logReadAheadPlayerAction('read_ahead_minimize','Controls','');
		read_ahead_switch_min_max();
	}

	function read_ahead_maximize(){
		setMinimized = false;
		logReadAheadPlayerAction('read_ahead_maximize','Controls','');
		read_ahead_switch_min_max();
	}

	function read_ahead_switch_min_max(forceSwitch){
		forceSwitch = forceSwitch != undefined ? forceSwitch : false;
		if (forceSwitch) { setMinimized = !setMinimized; }

		if (setMinimized) {
			$('#read_ahead_player_back').fadeOut();
			$('#read_ahead_player').addClass('minimize');
			$('.player-icons .fa-stack').removeClass('fa-lg').addClass('fa-sm');
			$('.player-icons .fa-minus').removeClass('fa-minus').addClass('fa-expand');
			logReadAheadPlayerAction('read_ahead_switch_min_max','Min','');
			//$('#read_ahead_player_max_min').each(function(){
			//	$(this).off('click');
			//	$(this).attr('onclick','read_ahead_maximize()');
			//});
		} else {
			$('#read_ahead_player_back').fadeIn();
			$('#read_ahead_player').removeClass('minimize');
			$('.player-icons .fa-stack').removeClass('fa-sm').addClass('fa-lg');
			$('.player-icons .fa-expand').removeClass('fa-expand').addClass('fa-minus');
			logReadAheadPlayerAction('read_ahead_switch_min_max','Max','');
			//$('#read_ahead_player_max_min').each(function(){
			//	$(this).off('click');
			//	$(this).attr('onclick','read_ahead_minimize()');
			//});
		}

	}

	function saveReadAheadPosition(){
		$.ajax({
			type:'POST',
			url:'/ajax/save_user_presentation_position.php',
			data: { 'id':2182,
					'position': currentPosition
				}
		})
		.done(function(results){
		})
		.fail(function( jqXHR, textStatus ) {
			alert( "Request failed: " + textStatus );
		});

	}

	function logLTIEndPresentation(action) {
		if (!logToLTI) {
			return;
		}

		$.ajax({
			type:'POST',
			url:'/lti/presentationEnded.php',
			data: { 'documentId':2182,
					'userId':0,
				}
		})
	}

	function logReadAheadPlayerAction(action,area,details){
		var d = new Date();
		var t = d.getTime();
		action = action != undefined ? action.trim() : 'UNKNOWN';
		area = area != undefined ? area.trim() : '';
		details = details != undefined ? details : '';

		// If we are about to show a new word, increase the number of keywords
		// reinforced so we can log that for the Dashboard page.
		if (area == 'Word') {
			window.keywordCount++;
		}

		$.ajax({
			type:'POST',
			url:'/logging/logPlayerAction.php',
			data: { 'documentId':2182,
					'userId':0,
					'playerAction':action,
					'playerArea':area,
					'details':details,
					'timestamp': t
				}
		})
		.done(function(results){
		})
		.fail(function( jqXHR, textStatus ) {
			alert( "Request failed: " + textStatus );
		});

	}