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forked:Mammalian PromoterCAD: Data Driven Design of Regulatory DNA for Mammals
jquery-1.7.1.min.js
jquery-ui-1.8.18.min.js
http://code.highcharts.com/highcharts.js
http://code.highcharts.com/modules/exporting.js
http://code.highcharts.com/highcharts-more.js

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forked:Mammalian PromoterCAD: Data Driven Design of Regulatory DNA for Mammals

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forked:Mammalian PromoterCAD: Data Driven Design of Regulatory DNA for Mammals

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forked:Mammalian PromoterCAD: Data Driven Design of Regulatory DNA for Mammals

var seqSize = 10000; //3000; //2000; //1000; //500;

if (typeof Application == "undefined" || !Application) {
	var Application = {};
}

Application.genocon = function() {
	this._init.apply(this, arguments);
};

Application.genocon.prototype = {
	
	CHAR_SEQ_EMPTY : "-",
	
	_baseSequence : null,
	_tooltip : null,
	_methodList : null,
	_appBaseLineSequence : null,
	_appMenuHandler : null,
	_validCharcters : ['A','T','C','G','-'],
	
	_default : {
		baseSequenceContainerId : "baseSequenceContainer",
		fixedSequenceClass : "fixedSequence",
		finishSequence : "finishSequence",
		finishSequenceContainer : "finishSequenceContainer",
		baseErrorMessageClass : "baseErrorMessage",
		errorMessageEnterSequence : "Please enter a sequence of minimum length {0}",
		errorMessageMaximumSequence : "Please enter a sequence of maximum length {0}",
		useButtonClass : "useButton",
		nextButtonClass : "nextButton",
		finishNowButtonClass : "finishNow",
		nextButtonContainerClass : "nextButtonContainer",
		collapseButton : "collapseButton",
		expandButton : "expandButton",
		removeButton : "removeButton",
		appContainerClass : "applicationContainer",
		appDataContainerClass : "applicationDataContainer",
		actionButtonContainer : "actionButtonContainer",
		actionResultContainer : "actionResultContainer",
		baseSequenceBoxClass : "baseSequenceBox",
		baseSequenceClass : "baseSequence",
		selectDataBaseList : "databaseList",
		selectMethodList : "optionList",
		databaseFilteringProperty : "#motif%20sequence",
		methodUrlProperty : "#application%20URL",
		baseSequenceMinLength : 31, //50,
		baseSequenceMaxLength : seqSize, //2000, //1000, //500,
		//applicationOptionClass : "applicationOptionRadio",
		analysisMethodComboClass : "analysisMethod",
		expressionDbComboClass : "expressionDb",
		dataColomboClass : "dataCol",
		analysisMethodContainer : "analysisMethodContainer",
		expressionDbContainer : "expressionDbContainer",
		dataColContainer : "dataColContainer",
		chkEmptySequenceId : "chkEmptySequnce",
		analysisMethodComboEmptyOptionText : "-- Select Analysis Method --",
		expressionDbComboEmptyOptionText : "-- Select Expression Database --",
		dataColColomboEmptyOptionText : "-- Select Data Collection --",
		manualMotifEntryToolName : "InputMotif",
		itemLabelPostfix : "Label",
		finishSequenceFixedClass : "finishSequenceFixed",
		repeatButtonClass : "repeatAgain",
		baseSequenceErrDivClass : "baseSequenceError"
	},
	
	_tag : {
		databaseTag : "database",
		methodTag : "method"
	},
	
	_tooltipName : {
		atGeneExpress : "atgenexpress",
		diurnal : "diurnal",
		selectDatabase : "selectdatabase",
		selectTool : "Select Tool",
		motifExpress : "motifexpress",
		motifCircatian : "motifcircadian",
		motifRank : "motifranking",
		motifQuery : "motifquery",
		inputMotif : "inputmotif",
		defaultSequence : "Base Sequence",
		//fixedSequence : "gacccttcctctatataaggaagttcatttcatttggagaggacctcgac",
		fixedSequence : "aggtctatataagcagagctctctggctaac",
		finishNow : "Finish Now",
		next : "Next",
		expressionDb : "Expression Database",
		analysisMethod : "Analysis Method",
		dataCollection : "Data Collection",
		baseSequence : "Base Sequence",
		finishNow : "Finish Now",
		startButton : "Start"
	},
	
	_init : function() {
		this._methodList = [];
		this._initToolTip();
		this._initDefaultSequence();
		this._initAppBaseLineSequence();
		this._initLoadScript();
		this._initUseButtonListener();
		this._initAppMenuHanndler();
		this._initAnalysisMethodListener();
		this._initExpressionDbListener();
		this._initDataCollectionListener();
		this._initEmptySequenceCheckBox();
	},
	
	_initToolTip : function() {
		this._tooltip = new Application.tooltip();
	},
	
	_initEmptySequenceCheckBox : function() {
		var self = this;
		$("#" + this._default.chkEmptySequenceId).click(function() {
			if ($(this).is(":checked")) {
				var textArea = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass)
				$(textArea).attr("value","");
				self._fillEmptyBaseSequence();
				$(textArea).attr("disabled",true);
				$("div." + self._default.baseSequenceErrDivClass).hide();
			} else {
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("disabled",false);
			}
		});
		/* following two lines were added to correct the behaviour, if user just pressed F5 button to 
           refresh the browser. in that case if previously checkbox is unnchecked, even after pressing
           F5, it remains unchecked in the new window
        */
		$("#" + this._default.chkEmptySequenceId).attr("checked","checked");
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("disabled",true);
	},
	
	_initDefaultSequence : function() {
		var self = this;
		this._fillEmptyBaseSequence();
		$baseInput = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass);
		$baseInput.attr("value",$baseInput.val());
		$baseInput.keyup(function() {
			$baseInput.attr("value", $baseInput.val());
		});
		$("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceBoxClass).scrollLeft(10000);
		var timer = new Application.timer();
		var applyToolTip = function() {
			var dToolTip = self._getToolTip(self._tooltipName.defaultSequence);
			var fToolTip = self._getToolTip(self._tooltipName.fixedSequence);
			var toolToolTip = self._getToolTip(self._tooltipName.selectTool);
			var analysisCmbToolTip = self._getToolTip(self._tooltipName.analysisMethod);
			var expDbToolTip = self._getToolTip(self._tooltipName.expressionDb);
			var dataCollToolTip = self._getToolTip(self._tooltipName.dataCollection);
			var startButToolTip = self._getToolTip(self._tooltipName.startButton);
			if (dToolTip && fToolTip) {
				var labelPostfix = self._default.itemLabelPostfix;
				//$("#tests").html(dataCollToolTip);
				//$("#tests").attr("title",$("#tests").html());
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("title", dToolTip);
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass + labelPostfix).attr("title", dToolTip);
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass).attr("title", fToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.analysisMethodComboClass).attr("title", analysisCmbToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.analysisMethodComboClass + labelPostfix).attr("title", analysisCmbToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.expressionDbComboClass).attr("title", expDbToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.expressionDbComboClass + labelPostfix).attr("title", expDbToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.dataColomboClass).attr("title", dataCollToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.dataColomboClass + labelPostfix).attr("title", dataCollToolTip);
				
				$("." + self._default.appContainerClass + " ." + self._default.selectMethodList).attr("title", toolToolTip);
				$("." + self._default.appContainerClass + " ." + self._default.selectMethodList + labelPostfix).attr("title", toolToolTip);
				
				$(" ." + self._default.useButtonClass).attr("title", startButToolTip);
			} else {
				timer.call(applyToolTip);
			}
		}
		applyToolTip();
	},
	
	_initAppBaseLineSequence : function() {
		this._appBaseLineSequence = new Application.baseLineSequence();
	},
	
	_initAppMenuHanndler : function() {
		this._appMenuHandler = new Application.MenuHandler()
	},
	
	_initLoadScript : function() {
		var self = this;
		var getFilesByTag = function(result) {
			$.each(result, function(workId, fileArray){
				$.each(fileArray, function(fileKey, fileName) {
					var getProperties = function(propertytList) {
						$.each(propertytList, function(propKey, propVal) {
							if (propVal.indexOf(self._default.methodUrlProperty) > -1) {
								self._loadPluginScriptList(workId, fileName, propVal);
								return false;
							}
						});
					}
					LinkData.getProperties(workId, fileName, getProperties);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.methodTag, getFilesByTag);
	},
	
	_initDefaultContainer : function() {
		this._initMethod();
		this._initActionButton();
		this._initMethodListener();
	},
	
	_initMethod : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Tool --</option>");
		$select.attr("title", self._getToolTip(self._tooltipName.selectTool));
		var getFilesByTag = function(result) {
			$.each(result, function(workId, fileArray){
				$.each(fileArray, function(fileKey, fileName) {
					var getSubjects = function(subjectList) {
						$.each(subjectList, function(subKey, subVal) {
							var label = self._getLabel(subVal);
							var tooltip = self._getToolTipByToolName(label);
							tooltip = (tooltip) ? tooltip : "";
							$select.append("<option value='" + label + "' title='" + tooltip + "'>" + label + "</option>");
							self._methodList.push(label);
						});
					}
					LinkData.getSubjects(workId, fileName, getSubjects);
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.methodTag, getFilesByTag);
	},
	
	_initActionButton : function() {
		var self = this;
		$("." + self._default.actionButtonContainer + " ." + self._default.collapseButton).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.appDataContainerClass).hide();
		});
		$("." + self._default.actionButtonContainer + " ." + self._default.expandButton).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.appDataContainerClass).show();
		});
		$("." + self._default.actionButtonContainer + " ." + self._default.removeButton).click(function() {
			if ($("." + self._default.appContainerClass).length == 1) {
				$("." + self._default.appContainerClass).hide();
				$("." + self._default.appContainerClass + " .actionResultContainer").html("");
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.useButtonClass).show();
			} else {
				$(this).closest("." + self._default.appContainerClass).remove();
			}
		});
	},
	
	_scrollDown : function() {
		$("html, body").animate({ scrollTop: $(document).height() }, 1000);
	},
	
	// tool listner
	_initMethodListener : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$select.change(function() {
			var selectedTool = $(this).val();
			if (selectedTool != "-1") {
				var parent = $(this).closest("." + self._default.appContainerClass);
				if (selectedTool == self._default.manualMotifEntryToolName) {
					//$(parent).find("." + self._default.applicationOptionClass).hide();
					self._showSelectedPlugin(null,$(this));
				} else {
					//self._clearWorkingArea(this);
					//self._initMotifExpressOptions(this);
					self._fillAnalysisMethodCombo(this);
					$(parent).find("." + self._default.analysisMethodContainer).show();
				}
				self._resetDataMiningCombos(this);
				self._scrollDown();
			}
		});
	},
	
	_makeTheDomChangeOfComboSelect : function(comboSelecter, value) {
		$(comboSelecter + " option").each(function(i){
        	var optionVal = $(this).val();
			if (optionVal == value) {
				$(this).attr("selected",true);
			}
    	});
	},
	
	_initAnalysisMethodListener : function() {
		var self = this;
		var selecter = "." + self._default.appContainerClass + " ." + self._default.analysisMethodComboClass;
		var $select = $(selecter);
		$select.change(function() {
			var selectedAnalysisMethod = $(this).val();
			if (selectedAnalysisMethod != "-1") {
				var parent = $(this).closest("." + self._default.appContainerClass);
				self._fillExpressionDBCombo(this);
				self._resetDataMiningCombos(this);
				$(parent).find("." + self._default.expressionDbContainer).show();
				self._scrollDown();
			}
		});
	},
	
	_initExpressionDbListener : function() {
		var self = this;
		var selector = "." + self._default.appContainerClass + " ." + self._default.expressionDbComboClass
		var $select = $(selector);
		$select.change(function() {
			var selectedExpressionDb = $(this).val();
			if (selectedExpressionDb != "-1") {
				var parent = $(this).closest("." + self._default.appContainerClass);
				self._fillDataCollectionCombo(this);
				self._resetDataMiningCombos(this);
				$(parent).find("." + self._default.dataColContainer).show();
				self._scrollDown();
			}
		});
	},
	
	_initDataCollectionListener : function() {
		var self = this;
		var selector = "." + self._default.appContainerClass + " ." + self._default.dataColomboClass;
		var $select = $(selector);
		$select.change(function() {
			var selectedDataCollection = $(this).val();
			if (selectedDataCollection != "-1") {
				self._showSelectedPlugin(selectedDataCollection,$(this));
				self._scrollDown();
			}
		});
	},
	
	_getSelectedTool : function(parentRef) {
		return $(parentRef).find("." + this._default.selectMethodList).val();
	},
	
	_getSelectedAnalysisMethod : function(parentRef) {
		var comboRef = $(parentRef).find("." + this._default.analysisMethodComboClass);
		if (comboRef.length > 0 && comboRef.is(":visible")) {
			return $(comboRef).val();
		} else {
			return "";
		}
	},
	/*
	_initMotifExpressOptions : function(context) {
		var self = this;
		var parent = $(context).closest("." + this._default.appContainerClass);
		//$(parent).find("." + self._default.applicationOptionClass).unbind('click');
		var selectedTool = $(context).val();
		if (selectedTool == "MotifExpress") {
			$(parent).find("." + self._default.applicationOptionClass).show();
			$(parent).find("." + self._default.applicationOptionClass).click(function() {
				var selectedDataCollection = $(parent).find("." + self._default.dataColomboClass);
				if ($(selectedDataCollection).is(":visible") && $(selectedDataCollection).val() != "-1") {
					self._showSelectedPlugin(selectedDataCollection.val(),$(this));
					//return;
				}	
			});
			// making motif max as the defaukt mthod
			$(parent).find("." + self._default.applicationOptionClass + " input[name=applicationOption]:checked")[0].checked=true;
		} else {
			$(parent).find("." + self._default.applicationOptionClass).hide();
		}
	},*/
	
	_resetDataMiningCombos : function(comboRef) {
		var parent = $(comboRef).closest("." + this._default.appContainerClass);
		var expressionDbContainer = $(parent).find("." + this._default.expressionDbContainer);
		var dataColContainer = $(parent).find(" ." + this._default.dataColContainer);
		var analysisMethodContainer = $(parent).find(" ." + this._default.analysisMethodContainer);
		var toolCombo = $(parent).find("." + this._default.selectMethodList);
		var comboClass = $(comboRef).attr("class");
		if (toolCombo.val() == this._default.manualMotifEntryToolName) {
			$(analysisMethodContainer).hide();
			$(expressionDbContainer).hide();
			$(dataColContainer).hide();
		} else {
			if (comboClass == this._default.selectMethodList) {
				$(analysisMethodContainer).show();
				$(expressionDbContainer).hide();
				$(dataColContainer).hide();
			} else if (comboClass == this._default.analysisMethodComboClass) {
				$(expressionDbContainer).hide();
				$(dataColContainer).hide();
			}
			$container = $(parent).find("." + this._default.actionResultContainer);
			$container.html("");
		}
		$(parent).find("." + this._default.finishSequenceContainer).hide()
		this._scrollDown();
		//$(parent).find("." + this._default.finishSequenceFixedClass).hide();
	},
	
	_showSelectedPlugin : function(selectedDataCollection,context) {
		var self = this;
		var info = null;
		if (selectedDataCollection) {
			info = this._appMenuHandler._getSelectedDbInfoUsingDataCollection(selectedDataCollection);
		}
		var parent = $(context).closest("." + this._default.appContainerClass);
		var method = $(parent).find("." + self._default.selectMethodList).val();
		var analysisMethod = $(parent).find("." + self._default.analysisMethodComboClass).val();
		$container = $(parent).find("." + self._default.actionResultContainer);
		$container.html("Loading...");
		//$(parent).find("." + this._default.applicationOptionClass).hide();
		$(parent).find("." + this._default.nextButtonContainerClass).hide();
		var date = new Date();
		var id = "container_id_" + date.getTime();
		//var appOption = $(parent).find("." + self._default.applicationOptionClass + " input[name=applicationOption]:checked").val();
		var fixedSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass).html();
		$container.attr("id", id);
		var func = function() {
			self._callback(parent, self);
		}
		var obj = {
			workId : (info) ? info.workId : "",
			fileName : (info) ? info.fileName : "",
			rankListWorkId : (info) ? info.rankListWorkId : "",
			plotingWorkId : (info) ? info.plotingWorkId : "",
			baseSequence : self._baseSequence,
			tooltip : self._tooltip,
			callback : func,
			//applicationOption : appOption,
			fixedSequence : fixedSeq,
			motifMethod : this._getSelectedAnalysisMethod(parent),
			dataColl : selectedDataCollection,
			analysisMethod : analysisMethod
		};
		
		eval(method)(id, obj);
		self._scrollDown();
	},
	
	_fillAnalysisMethodCombo : function(selectToolCmbRef) {
		var parent = $(selectToolCmbRef).closest("." + this._default.appContainerClass);
		var selectedTool = $(selectToolCmbRef).val();
		var analysisMethods = this._appMenuHandler._getFilteredDistinctAnalysisMethods(selectedTool);
		var analysisMethodCmb = $(parent).find("." + this._default.analysisMethodComboClass);
		this._fillCombo(analysisMethods, analysisMethodCmb, this._default.analysisMethodComboEmptyOptionText, this._tooltipName.analysisMethod);
	},
	
	_fillExpressionDBCombo : function(analysisMethodCmbRef) {
		var parent = $(analysisMethodCmbRef).closest("." + this._default.appContainerClass);
		var selectedTool = this._getSelectedTool(parent);
		var selectedAnalysisMethod = $(analysisMethodCmbRef).val();
		var expressionDbs = this._appMenuHandler._getFilteredDistinctExpressionDbs(selectedTool,selectedAnalysisMethod);
		var analysisMethodCmb = $(parent).find("." + this._default.expressionDbComboClass);
		this._fillCombo(expressionDbs, analysisMethodCmb, this._default.expressionDbComboEmptyOptionText, this._tooltipName.expressionDb);
	},
	
	_fillDataCollectionCombo : function(expressionDbRef) {
		var parent = $(expressionDbRef).closest("." + this._default.appContainerClass);
		var selectedTool = this._getSelectedTool(parent);
		var selectedAnalysisMethod = this._getSelectedAnalysisMethod(parent);
		var selectedExpressionDb = $(expressionDbRef).val();
		var dataCollections = this._appMenuHandler._getFilteredDistinctDataCollections(selectedTool,selectedAnalysisMethod,selectedExpressionDb);
		var dataColCmb = $(parent).find("." + this._default.dataColomboClass);
		this._fillCombo(dataCollections, dataColCmb, this._default.dataColColomboEmptyOptionText, this._tooltipName.dataCollection);
	},
		
	_fillCombo : function(optionsArr, cmbRef, firstOptionText, firstOptionToolTipKey) {
		$(cmbRef).empty();
		var toolTip = this._tooltip.getByKey(firstOptionToolTipKey);
		$(cmbRef).append("<option value='-1' title='"+ toolTip +"'>"+ firstOptionText +"</option>");
		for (var index = 0 ; index < optionsArr.length ; index++) {
			var option = optionsArr[index];
			toolTip = this._tooltip.getByKey(option);
			$(cmbRef).append("<option value='"+ option + "' title='"+ toolTip +"'>"+ option +"</option>");
		}	
	},

_fillEmptyBaseSequence : function() {
		var self = this, sb = [];
		for (var i = 0; i < self._default.baseSequenceMaxLength; i++) {
			sb[sb.length] = self.CHAR_SEQ_EMPTY;
		}
		$baseInput = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass);
		$baseInput.val(sb.join(""));
	},
	
	_loadPluginScriptList : function(workId, fileName, property) {
		var getTripleList = function(tripleList) {
			$.each(tripleList, function(tKey, tVal) {
				LinkDataUtil.loadScript(tVal.object);
			});
		}
		LinkData.getTriplesByProperty(workId, fileName, property, getTripleList);
	},
	
	_changeMethodList : function(dbKey) {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$select.attr("title", self._getToolTip(self._tooltipName.selectTool));
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Tool --</option>");
		if (dbKey == -1) {
			return;
		}
		var arr = dbKey.split("|");
		var workId = arr[0];
		var fileName = arr[1];
		$.each(self._methodList, function(key, method) {
			self._addValidMethod($select, workId, fileName, method);
		});
	},
	
	_addValidMethod : function($select, workId, fileName, method) {
		var self = this;
		var getFilesByTag = function(fileList) {
			if (!fileList) {
				return;
			}
			$.each(fileList, function(fKey, fName) {
				if (fName === fileName) {
					var tooltip = self._getToolTipByToolName(method);
					tooltip = (tooltip) ? tooltip : "";
					$select.append("<option value='" + method + "' title='" + tooltip + "'>" + method + "</option>");
					return false;
				}
			});
		}
		LinkData.getFilesByTag(workId, method, getFilesByTag);
	},
	
	_initUseButtonListener : function() {
		var self = this;
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.useButtonClass).click(function() {
			self._initDefaultContainer();
			$txtSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass);
			$fixedSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass);
			self._hideError();
			if ($txtSeq.val().length > self._default.baseSequenceMaxLength) {
				self._showError(self._default.errorMessageMaximumSequence.replace("{0}", self._default.baseSequenceMaxLength));
				return;
			}
			self._showWarningForNonStandardCharsIfExists();
			if ($txtSeq.val().length < self._default.baseSequenceMaxLength) {
				var tmpVal = $txtSeq.val();
				var eVal = self._getExtraDefaultSequence(self._default.baseSequenceMaxLength - $txtSeq.val().length);
				$txtSeq.val(eVal + tmpVal);
				//$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("size", 500);
				//$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("size", 1000);
				//$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("size", 2000);
				$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass).attr("size", seqSize);
			}
			self._baseSequence = $txtSeq.val().toString().toLowerCase() + $fixedSeq.html();
			if (!self._baseSequence || self._baseSequence.length < self._default.baseSequenceMinLength) {
				self._showError(self._default.errorMessageEnterSequence.replace("{0}", self._default.baseSequenceMinLength));
			} else {
				//$txtSeq.attr('readonly', true).addClass("noborder");
				$(this).hide();
				$("." + self._default.appContainerClass).show();
				$("." + self._default.appContainerClass + " ." + self._default.expressionDbContainer).hide();
		    	$("." + self._default.appContainerClass + " ." + self._default.dataColContainer).hide();
				$("." + self._default.appContainerClass + " ." + self._default.analysisMethodContainer).hide();
				$("." + self._default.appContainerClass + " ." + self._default.nextButtonContainerClass).hide();
				$("." + self._default.appContainerClass + " ." + self._default.finishSequenceContainer).hide()
			}
		});
	},
	
	_showWarningForNonStandardCharsIfExists : function() {
		var found = false;
		var txtSeq = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass).val();
		for (var i = 0 ; i < txtSeq.length ; i++) {
			var char = txtSeq.charAt(i).toString().toUpperCase();
			if (this._validCharcters.indexOf(char) == -1) {
				$("div." + this._default.baseSequenceErrDivClass).show();
				found = true;
				break;
			}
		}
		if (found == false) {
			$("div." + this._default.baseSequenceErrDivClass).hide();
		}
	},
	
	_callback : function(parent, self) {
		if (self._isSelectedManualMotif(parent)) {
			$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).hide();
			$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).hide();
			//self._initNextButtonListener();
		} else {
			$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).show();
			$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).attr("title", self._getToolTip(self._tooltipName.finishNow));
			$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).show();
			self._initFinishNowButtonListener();
		}
		$(parent).find("." + self._default.nextButtonContainerClass).show();
		$(parent).find("." + self._default.finishSequenceContainer).hide();
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).attr("title", self._getToolTip(self._tooltipName.next));
		$(parent).find("." + self._default.nextButtonContainerClass).show();
		self._initNextButtonListener();
		self._initRepeatButtonListner();
	},
	
	_isSelectedManualMotif : function(parent) {
		var toolCombo = $(parent).find("." + this._default.selectMethodList);
		var selectedTool = toolCombo.val();
		if (selectedTool == this._default.manualMotifEntryToolName) {
			return true;
		} else {
			return false;
		}
	},
	
	_initNextButtonListener : function() {
		var self = this;
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).click(function() {
			$parent = $(this).closest("." + self._default.appContainerClass);
			$parent.find("." + self._default.nextButtonContainerClass).hide();
			$($parent).find("." + self._default.finishSequenceContainer).hide()
			var clone = $parent.clone(true);
			//$(clone).find("." + self._default.applicationOptionClass).hide();
			var text = $(clone).find(".replaceSequence").text();
			if (text && text.trim().length != 0) {
				self._baseSequence = text;
			}
			$(clone).find("." + self._default.actionResultContainer).html("");
			$(clone).find("." + self._default.nextButtonContainerClass).hide();
			$(clone).find("." + self._default.expressionDbContainer).hide();
		    $(clone).find(" ." + self._default.dataColContainer).hide();
			$(clone).find(" ." + self._default.analysisMethodContainer).hide();
			$parent.parent().append(clone);
			self._scrollDown();
		});
	},
	
	_initFinishNowButtonListener : function() {
		var self = this;
		$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.finishNowButtonClass).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.nextButtonContainerClass).hide();
			$(parent).find("." + self._default.finishSequenceContainer).hide()
			var gene = $(parent).find(".replaceSequence .gene").val();
			var geneType = $(parent).find(".replaceSequence .geneType").val();
			if (gene && geneType) {
				var callback = function(bSequence) {
					self._showFinishedBaseSequence(parent, bSequence);
				}
				//self._appBaseLineSequence.getBaseSequence(gene, geneType, callback);
				self._appBaseLineSequence._getBaseSequence(gene, callback);
			} else {
				self._showFinishedBaseSequence(parent,self._baseSequence);
			}
			self._scrollDown();
		});
	},
	
	_initRepeatButtonListner : function() {
		var self = this;
		$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.repeatButtonClass).click(function() {
			$parent = $(this).closest("." + self._default.appContainerClass);
			$parent.find("." + self._default.nextButtonContainerClass).hide();
			$($parent).find("." + self._default.finishSequenceContainer).hide()
			var clone = $parent.clone(true);
			var text = $(clone).find(".replaceSequence").text();
			if (text && text.trim().length != 0) {
				self._baseSequence = text;
			}
			$(clone).find("." + self._default.actionResultContainer).html("");
			$(clone).find("." + self._default.nextButtonContainerClass).hide();
			// setting the values
			var tool = $($parent).find("." + self._default.selectMethodList).val();	
			var expressionDb = $($parent).find("." + self._default.expressionDbComboClass).val();
			//var dataCollection = $($parent).find("." + self._default.dataColomboClass).val();
			var analysisMethod = $($parent).find("." + self._default.analysisMethodComboClass).val();
			$(clone).find("." + self._default.selectMethodList).val(tool);
			$(clone).find("." + self._default.expressionDbComboClass).val(expressionDb);
		    //$(clone).find(" ." + self._default.dataColomboClass).val(dataCollection);
			$(clone).find(" ." + self._default.analysisMethodComboClass).val(analysisMethod);
			$parent.parent().append(clone);
			self._scrollDown();
		});
	},
	
	_showFinishedBaseSequence : function(parent, bSequence) {
		var self = this;
		var defaultSequence = $(parent).find(".replaceSequence").text()
		$(parent).find(".wrappedSequenceMotif").hide();	
		var html = self._getFinishedBaseSequence(defaultSequence, bSequence);
		var fixedSequence = self._getFixedSequence();
		$(parent).find("." + self._default.finishSequenceContainer).show();
		$(parent).find("." + self._default.finishSequenceFixedClass).html(fixedSequence);
		//$(parent).find("." + self._default.finishSequenceFixedClass).show();
		$(parent).find("." + self._default.finishSequence).html(html);
		$(parent).find("." + self._default.finishSequence).scrollLeft(10000);
	},
	
	_getFixedSequence : function() {
		var fixedSequence = $("#" + this._default.baseSequenceContainerId + " ." + this._default.fixedSequenceClass).html();
		return fixedSequence;
	},
	
	_getFinishedBaseSequence : function(defaultSequence, bSequence) {
		var self = this, sb = [];
		var fixedSequence = this._getFixedSequence();
		var uptoFixedSequence = defaultSequence.length - fixedSequence.length;
		for (var i = 0; i < defaultSequence.length; i++) {
			if (i > uptoFixedSequence - 1) {
				continue;
			}
			var dChar = defaultSequence.charAt(i);
			var bChar = bSequence.charAt(i);
			if (bChar) {
				if (dChar !== self.CHAR_SEQ_EMPTY) {
					sb[sb.length] = "<span class='highlight-sequence'><span class='replace'>" + dChar + "</span></span>";
				} else {
					sb[sb.length] = bChar.toLowerCase();
				}
			} else {
				sb[sb.length] = "<span class='highlight-sequence'><span class='replace'>" + dChar + "</span></span>";
			}
		}
		return sb.join("");
	},
	
	_getExtraDefaultSequence : function(count) {
		var self = this, sb = [];
		for (var i = 0; i < count; i++) {
			sb[sb.length] = self.CHAR_SEQ_EMPTY;
		}
		return sb.join("");
	},
	
	_getDatabaseOptionKey : function(workId, fileName) {
		return workId + "|" + fileName;
	},
	
	_getLabel : function(value) {
		var propLabel = value;
		var arr = value.split("#");
		if (arr.length > 1) {
			propLabel = decodeURIComponent(arr[1]);
		}
		return propLabel;
	},
	
	_showError : function(message) {
		var self = this;
		$errMsgEl = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseErrorMessageClass);
		$errMsgEl.html(message);
		$errMsgEl.show();
	},
	
	_hideError : function() {
		var self = this;
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.baseErrorMessageClass).hide();
	},
	
	_getToolTipByFileName : function(fileName) {
		var self = this;
		if (fileName) {
			if (fileName.toLowerCase().indexOf(self._tooltipName.atGeneExpress) > -1) {
				return self._getToolTip(self._tooltipName.atGeneExpress);
			} else if (fileName.toLowerCase().indexOf(self._tooltipName.diunal) > -1) {
				return self._getToolTip(self._tooltipName.diunal);
			}
		}
	},
	
	_getToolTipByToolName : function(tool) {
		var self = this;
		if (tool) {
			if (tool.toLowerCase().indexOf(self._tooltipName.motifExpress) > -1) {
				return self._getToolTip(self._tooltipName.motifExpress);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.motifCircatian) > -1) {
				return self._getToolTip(self._tooltipName.motifCircatian);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.motifRank) > -1) {
				return self._getToolTip(self._tooltipName.motifRank);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.motifQuery) > -1) {
				return self._getToolTip(self._tooltipName.motifQuery);
			} else if (tool.toLowerCase().indexOf(self._tooltipName.inputMotif) > -1) {
				return self._getToolTip(self._tooltipName.inputMotif);
			}
		}
	},
	
	_getToolTip : function(key) {
		return this._tooltip.getByKey(key);
	}
	
};

Application.MenuHandler = function() {
	this._init.apply(this,arguments);
}

Application.MenuHandler.prototype = {
	
	_fullList : [],
	_currentFilteredList : [],
	_workId : null,
	_fileName : null,
	_fileProperties : null,
	
	_properties : {
		motifAnalysisMethod : "motif%20analysis%20method",
		geneExpressionData : "gene%20expression%20data",
		menuDisplayName : "menu%20display%20name",
		toolsList : "tool%20list",
		workIdInTest : "test.linkdata.org",
		workIdPublic : "linkdata.org",
		ranklistWorkIdTest : "rank%20list%20test.linkdata.org",
		ranklistWorkIdPublic : "rank%20list%20linkdata.org",
		plotingDataWorkIdTest :"plot%20in%20test.linkdata.org",
		plotingDataWorkIdPublic :"plot%20in%20linkdata.org"
    },
	
	_tags : {
		menuDataSourceTag : "menu"
	},
	
	_defaults : {
		linkdataTestUrl : "test.linkdata.org",
		linkdataPublicUrl : "linkdata.org",
	},
	
	_init : function(args) {
		this._initMenuDataSource();
	},
	
	_fillFileProperties : function() {
		var self = this;
		var setProperties = function(props) {
			self._fileProperties = props;
		};
		LinkData.getProperties(this._workId,this._fileName,setProperties);
	},
	
	_initMenuDataSource : function() {
		var self = this;
		var foundMenuFiles = [];
		var loadMenuFiles = function(resultList) {
			$.each(resultList, function(wId, fileList) {
				$.each(fileList, function(fileKey, fName) {
					var obj = {
						workId : wId,
						fileName : fName
					};
					foundMenuFiles.push(obj);
				});
			});
			self._foundMenuFiles = foundMenuFiles;
			self._loadMenuFileContent(foundMenuFiles);
			self._fillFileProperties();
		};
		LinkData.getFilesByTag(null, this._tags.menuDataSourceTag, loadMenuFiles);
	},
	
	_loadMenuFileContent : function(menuFiles) {
		var self = this;
		var addFileContent = function(triples) {
			for (var index = 0 ; index < triples.length ; index++) {
				self._fullList.push(triples[index]);
			}
		};
		if (menuFiles.length > 1) {
			alert("There can be only one file that can be tagged with 'menu'");
			return;
		}
		if (menuFiles.length == 0) {
			return;
		}
		var obj = menuFiles.shift(); // removing the first element
		this._fileName = obj.fileName;
		this._workId = obj.workId;
		LinkData.getTriples(this._workId,this._fileName,addFileContent,{start:1, end:2000});
	},
	
	
	_getFilteredAnalysisMethodTriples : function(toolName) {
		if (!(toolName)) return this._fullList;
		this._currentFilteredList = [];
		var listByTool = this._getTriplesByProperty(this._properties.toolsList,this._fullList);
		if (!listByTool) return null;
		var filteredList = [];
		for (var index = 0 ; index < listByTool.length ; index++) {
			var triple = listByTool[index];
			if (triple.object) {
				var toolList = triple.object.split(",");
				for (var index1 = 0 ; index1 < toolList.length ; index1++) {
					var tool = toolList[index1];
					if (tool.trim() == toolName.trim()) {
						var subject = triple.subject;
						var otherPropTripleList = this._getTriplesBySubject(subject);
						for (var index1 = 0 ; index1 < otherPropTripleList.length ; index1++) {
							var propTriple = otherPropTripleList[index1];
							//this._currentFilteredList.push(propTriple);
							filteredList.push(propTriple);
						}
						break;
					}
				}
			}
		}
	    return filteredList;
	},
	
	_getFilteredDistinctAnalysisMethods : function(toolName) {
		var filteredList = this._getFilteredAnalysisMethodTriples(toolName);
		this._currentFilteredList = filteredList;
		var distinctList = this._getDistinctObjectList(this._properties.motifAnalysisMethod,filteredList);
		return distinctList;
	},
		
	_getFilteredExpressionDbTriples : function(toolName,analysisMethodName) {
		var listByTool = this._getFilteredAnalysisMethodTriples(toolName);
		var listByAnalysisMethod = this._getTriplesByProperty(this._properties.motifAnalysisMethod,listByTool);
		if (!listByAnalysisMethod) return null;
		var filteredList = [];
		for (var index = 0 ; index < listByAnalysisMethod.length ; index++) {
			var triple = listByAnalysisMethod[index];
			if (triple.object) {
				var analysisMethod = triple.object;
				if (analysisMethod.trim() == analysisMethodName.trim()) {
					var subject = triple.subject;
					var otherPropTripleList = this._getTriplesBySubject(subject);
					for (var index1 = 0 ; index1 < otherPropTripleList.length ; index1++) {
						var propTriple = otherPropTripleList[index1];
						//this._currentFilteredList.push(propTriple);
						filteredList.push(propTriple);
					}
				}
			}
		}
		return filteredList
	},
	
	_getFilteredDistinctExpressionDbs : function(toolName,analysisMethodName) {
		var filteredList = this._getFilteredExpressionDbTriples(toolName,analysisMethodName);
		this._currentFilteredList = filteredList;
		var distinctList = this._getDistinctObjectList(this._properties.geneExpressionData,filteredList);
		return distinctList;
	},
		
	_getFilteredDataCollectionTriples : function(toolName,analysisMethodName,expressionDbName) {
		var listByExpDbs = this._getFilteredExpressionDbTriples(toolName,analysisMethodName);
		var listByGeneExp = this._getTriplesByProperty(this._properties.geneExpressionData,listByExpDbs);
		if (!listByGeneExp) return null;
		var filteredList = [];
		for (var index = 0 ; index < listByGeneExp.length ; index++) {
			var triple = listByGeneExp[index];
			if (triple.object) {
				var exprssionDb = triple.object;
				if (exprssionDb.trim() == expressionDbName.trim()) {
					var subject = triple.subject;
					var otherPropTripleList = this._getTriplesBySubject(subject);
					for (var index1 = 0 ; index1 < otherPropTripleList.length ; index1++) {
						var propTriple = otherPropTripleList[index1];
						//this._currentFilteredList.push(propTriple);
						filteredList.push(propTriple);
					}
				}
			}
		}
		return filteredList;
	},
		
	_getFilteredDistinctDataCollections : function(toolName,analysisMethodName,expressionDbName) {
		var filteredList = this._getFilteredDataCollectionTriples(toolName,analysisMethodName,expressionDbName);
		this._currentFilteredList = filteredList;
		var distinctList = this._getDistinctObjectList(this._properties.menuDisplayName,filteredList);
		return distinctList;
	},
	
	_getSelectedDbInfoUsingDataCollection : function(dataCollectionName) {
		var matchingList = [];
		var outObj = null;
		var listByDataCollection = this._getTriplesByProperty(this._properties.menuDisplayName,this._currentFilteredList);
		if (!listByDataCollection) return null;
		for (var index = 0 ; index < listByDataCollection.length ; index++) {
			var triple = listByDataCollection[index];
			var dataCollection = triple.object;
			if (dataCollection == dataCollectionName) {
				matchingList.push(triple);
			}
		}
		if (matchingList.length > 1) {
			// this a error. because there can be only one matching triple
			alert("Data file error");
		} else {
			// getting other triples for found one
			var subject = matchingList.shift().subject;
			var workId, rankWorkId, plotingWorkId = null;
			//
			//var geneTranscript = null;				
			//
			var otherPropTripleList = this._getTriplesBySubject(subject);
			var workIdProperty = this._getWorkIdProperty();
			var rankWorkIdProp = this._getRankingWorkIdProperty();
			var plotingWorkIdProp = this._getPlotingWorkIdProperty();
			for (var index=0 ; index < otherPropTripleList.length ; index++) {
				var triple = otherPropTripleList[index];
				var prop = this._getProperty(triple.property);
				if (workIdProperty == prop) {
					workId = triple.object;
				}
				if (rankWorkIdProp == prop) {
					rankWorkId = triple.object;
				}
				if (plotingWorkIdProp == prop) {
					plotingWorkId = triple.object;
				}
				//
				//if ("transcript" == prop) {
				//	geneTranscirpt = triple.object;
				//}
				//
				//if (workId && rankWorkId && plotingWorkId && geneTranscript) {
				if (workId && rankWorkId && plotingWorkId) {
					break;
				}
			}
			var workIdComps = workId.split("/");
			var rankWorkIdComps = rankWorkId.split("/");
			var plotingWorkIdComps = plotingWorkId.split("/");
			var subjectComps = subject.split("#");
			outObj = {
				fileName : subjectComps[subjectComps.length-1],
				workId : workIdComps[workIdComps.length-1],
				rankListWorkId : rankWorkIdComps[rankWorkIdComps.length-1],
				plotingWorkId : plotingWorkIdComps[plotingWorkIdComps.length-1]
			};
		}
		return outObj;
	},
	
	_getProperty : function(propertyUrl) {
		var comps = propertyUrl.split("#");
		return comps[comps.length-1];
	},
	
	_getWorkIdProperty : function() {
		var hostName = window.location.hostname;
		if (hostName.indexOf(this._defaults.linkdataTestUrl) != -1) {
			return this._properties.workIdInTest;
		} else if (hostName.indexOf(this._defaults.linkdataPublicUrl) != -1) {
			return this._properties.workIdPublic;
		}
	},
	
	_getRankingWorkIdProperty : function() {
		var hostName = window.location.hostname;
		if (hostName.indexOf(this._defaults.linkdataTestUrl) != -1) {
			return this._properties.ranklistWorkIdTest;
		} else if (hostName.indexOf(this._defaults.linkdataPublicUrl) != -1) {
			return this._properties.ranklistWorkIdPublic;
		}
	},
	
	_getPlotingWorkIdProperty : function() {
		var hostName = window.location.hostname;
		if (hostName.indexOf(this._defaults.linkdataTestUrl) != -1) {
			return this._properties.plotingDataWorkIdTest;
		} else if (hostName.indexOf(this._defaults.linkdataPublicUrl) != -1) {
			return this._properties.plotingDataWorkIdPublic;
		}
	},
	
	_getTriplesByProperty : function(propName,currentList) {
		/*
          this function first will find the triple with the passed property and then
		  this will take the subject of it and will find other properties of that
          subject
		*/
		var filteredList = [];
		//var currentList = this._getCurrentUsingList();
		for (var index = 0 ; index < currentList.length ; index++) {
			var triple = currentList[index];
			var prop = this._getProperty(triple.property);
			if (prop == propName) {
				filteredList.push(triple);
			}
		}
		return filteredList;
	},
	
	_getTriplesBySubject : function(subject) {
		var filteredList = [];
		var currentList = this._getCurrentUsingList();
		for (var index = 0 ; index < currentList.length ; index++) {
			var triple = currentList[index];
			var triSubject = triple.subject;
			if (triSubject.trim() == subject.trim()) {
				filteredList.push(triple);
			}
			if (filteredList.length == this._fileProperties.length) {
				break;
			}
		}
		return filteredList;
	},
	
	// returns a string array
	_getDistinctObjectList : function(propName,currentList) {
		var distinctList = [];
		for (var index = 0 ; index < currentList.length ; index++) {
			var triple = currentList[index];
			var prop = triple.property;
			if (prop && prop.indexOf(propName) != -1) {
				var objVal = triple.object;
				if (distinctList.indexOf(objVal) == -1) {
					distinctList.push(objVal);
				}
			}
		}
		return distinctList;
	},
	
	_getCurrentUsingList : function() {
		if (this._currentFilteredList.length == 0) {
			return this._fullList;
		} else {
			return this._currentFilteredList;
		}
	},
}
/*	
Application.baseLineSequence = function() {
	this._init.apply(this, arguments);
};

Application.baseLineSequence.prototype = {
	
	_attedSequenceInfo : null,
	_ppdbSequenceInfo : null,
	
	_default : {
		sequenceProperty : "baseline%20sequence"
	},
	
	_tag : {
		attedBaseSequenceTag : "atted_baseLineSequence",
		ppdbBaseSequenceTag : "ppdb_baseLineSequence"
	},
	
	_init : function() {
		this._attedSequenceInfo = {};
		this._ppdbSequenceInfo = {};
		this._initBaseSequenceFile();
	},
	
	_initBaseSequenceFile : function() {
		this._initAttedBaseSequenceFile();
		this._initPpdbBaseSequenceFile();
	},
	
	_initAttedBaseSequenceFile : function() {
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._initAttedInfo(workId, fileName);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.attedBaseSequenceTag, getFilesByTag);
	},
	
	_initPpdbBaseSequenceFile : function() {
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._initPpdbInfo(workId, fileName);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.ppdbBaseSequenceTag, getFilesByTag);
	},
	
	_initAttedInfo : function(workId, fileName) {
		var self = this;
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				var propOnly = pValue.split("#")[1];
				if (propOnly == self._default.sequenceProperty) {
					self._attedSequenceInfo.workId = workId;
					self._attedSequenceInfo.fileName = fileName;
					self._attedSequenceInfo.property = pValue;
					return false;
				}
			});
		}
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_initPpdbInfo : function(workId, fileName) {
		var self = this;
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				var propOnly = pValue.split("#")[1];
				if (propOnly == self._default.sequenceProperty) {
					self._ppdbSequenceInfo.workId = workId;
					self._ppdbSequenceInfo.fileName = fileName;
					self._ppdbSequenceInfo.property = pValue;
					return false;
				}
			});
		}
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_getAttedSubjectUrl : function(gene) {
		return "http://atted.jp/data/locus/" + gene + ".html";
	},
	
	_getPpdbSubjectUrl : function(gene) {
		return "http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/display.cgi?organism=At&gene=" + gene;
	},
	
	_getAttedBaseSequence : function(gene, callback) {
		var self = this;
		var workId = self._attedSequenceInfo.workId;
		var fileName = self._attedSequenceInfo.fileName;
		var property = self._attedSequenceInfo.property;
		var subject = self._getAttedSubjectUrl(gene);
		var getObjects = function(objList) {
			callback(objList[0]);
		}
		LinkData.getObjects(workId, fileName, subject, property, getObjects);
	},
	
	_getPpdbBaseSequence : function(gene, callback) {
		var self = this;
		var workId = self._ppdbSequenceInfo.workId;
		var fileName = self._ppdbSequenceInfo.fileName;
		var property = self._ppdbSequenceInfo.property;
		var subject = self._getPpdbSubjectUrl(gene);
		var getObjects = function(objList) {
			callback(objList[0]);
		}
		LinkData.getObjects(workId, fileName, subject, property, getObjects);
	},
	
	getBaseSequence : function(gene, geneType, callback) {
		var self = this;
		if ("ATTED" === geneType) {
			self._getAttedBaseSequence(gene, callback);
		} else if ("PPDB" === geneType) {
			self._getPpdbBaseSequence(gene, callback);
		} else {
			// error
		}
	}
};
*/
Application.baseLineSequence = function() {
	this._init.apply(this,arguments);
}
	
Application.baseLineSequence.prototype = {
	
	_baseLineSeqFileInfo : null,
	
	_default : {
		sequenceProperty : "promoter%20sequence",
		linkdataTestUrl : "test.linkdata.org",
		linkdatapublicUrl : "linkdata.org"
	},
	
	_tag : {
		baseSequenceTag : "promoter_sequence",
	},
	
	_init : function() {
		this._findBaseLineSequenceFile();
		this._baseLineSeqFileInfo = {};
	},
	
	_findBaseLineSequenceFile : function() {
		// looking one tagged file only
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._initBaseLineSequenceFileInfo(workId, fileName);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.baseSequenceTag, getFilesByTag);
	},
	
	_initBaseLineSequenceFileInfo : function(workId, fileName) {
		var self = this;
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				var propOnly = pValue.split("#")[1];
				if (propOnly == self._default.sequenceProperty) {
					self._baseLineSeqFileInfo.workId = workId;
					self._baseLineSeqFileInfo.fileName = fileName;
					self._baseLineSeqFileInfo.property = pValue;
					return false;
				}
			});
		};
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_getSubject : function(gene) {
		var hostName = window.location.hostname;
		var subject = null;
		gene = gene.toUpperCase();
		if (hostName.indexOf(this._default.linkdataTestUrl) != -1) {
			subject = this._default.linkdataTestUrl + "/resource/" + this._baseLineSeqFileInfo.workId + "#" + gene;
		} else if (hostName.indexOf(this._default.linkdatapublicUrl) != -1) {
			subject = this._default.linkdatapublicUrl + "/resource/" + this._baseLineSeqFileInfo.workId + "#" + gene;;
		}
		return "http://" + subject;
	},
	
	_getBaseSequence : function(gene, callback) {
		var self = this;
		var workId = self._baseLineSeqFileInfo.workId;
		var fileName = self._baseLineSeqFileInfo.fileName;
		var property = self._baseLineSeqFileInfo.property;
		var subject = self._getSubject(gene);
		var getObjects = function(objList) {
			callback(objList[0]);
		}
		LinkData.getObjects(workId, fileName, subject, property, getObjects);
	}
}

Application.tooltip = function() {
	this._init.apply(this, arguments);
};

Application.tooltip.prototype = {
	
	_toolTipList : null,
	
	_default : {
		explanationProperty : "explanation"
	},
	
	_init : function() {
		this._toolTipList = [];
		this._initToolTip();
	},
	
	_initToolTip : function() {
		var self = this;
		var getFilesByTag = function(resultList) {
			$.each(resultList, function(workId, fileList) {
				$.each(fileList, function(fileKey, fileName) {
					self._getFilePropertyList(workId, fileName);
				});
			});
		}
		LinkData.getFilesByTag(null, "tooltip", getFilesByTag);
	},
	
	_getFilePropertyList : function(workId, fileName) {
		var self = this;
		var index = new Application.index(1, 10000);
		var getProperties = function(propertyList) {
			$.each(propertyList, function(pKey, pValue) {
				if (pValue.indexOf(self._default.explanationProperty) > -1) {
					self._getSubjectList(workId, fileName, pValue, index);
					return false;
				}
			});
		}
		LinkData.getProperties(workId, fileName, getProperties);
	},
	
	_getSubjectList : function(workId, fileName, property, index) {
		var self = this;
		var getSubjects = function(subjectList) {
			self._getPropertyList(subjectList, workId, fileName, property, index);
		}
		LinkData.getSubjects(workId, fileName, getSubjects, index);
	},
	
	_getPropertyList : function(subjectList, workId, fileName, property, index) {
		var self = this;
		var getTriplesByProperty = function(tripleList) {
			self._addToolTipToList(subjectList, tripleList, workId, fileName, property, index);
		}
		LinkData.getTriplesByProperty(workId, fileName, property, getTriplesByProperty, index);
	},
	
	_addToolTipToList : function(subjectList, tripleList, workId, fileName, property, index) {
		var self = this;
		for (var i = 0; i < subjectList.length; i++) {
			var key = self._getLabelAfterHash(subjectList[i]);
			if (tripleList[i]) {
				var value = tripleList[i].object;
				self._addToolTip(key, value);
			}
		}
		if (subjectList && subjectList.length == index.getItemCount()) {
			self._getSubjectList(workId, fileName, property, index.increment());
		}
	},
	
	_addToolTip : function(key, tooltip) {
		var obj = {};
		obj.key = key;
		obj.tooltip = tooltip;
		this._toolTipList.push(obj);
	},
	
	getByKey : function(key) {
		var self = this, tooltip;
		$.each(self._toolTipList, function(objKey, obj) {
			if (obj.key.toString().toLowerCase() === key.toString().toLowerCase()) {
				tooltip = obj.tooltip;
				return false;
			}
		});
		return (tooltip) ? tooltip : "";
	},
	
	_getLabelAfterHash : function(value) {
		var propLabel = value;
		var arr = value.split("#");
		if (arr.length > 1) {
			propLabel = decodeURIComponent(arr[1]);
		}
		return propLabel;
	}
};

Application.index = function() {
	this._init.apply(this, arguments);
}

Application.index.prototype = {
	
	_start : null,
	_end : null,
	
	_init : function(start, end) {
		this._start = start;
		this._end = end;
	},
	
	getIndex : function() {
		return {start : this._start, end : this._end};
	},
	
	getItemCount : function() {
		return (this._end - this._start + 1);
	},
	
	increment : function() {
		var itemCount = this.getItemCount();
		this._start = this._start + itemCount;
		this._end = this._end + itemCount;
		return {start : this._start, end : this._end};
	},
	
	getStartIndex : function() {
		return this._start;
	},
	
	getEndIndex : function() {
		return this._end;
	}
	
};

Application.timer = function() {
	this._init.apply(this, arguments);
};

Application.timer.prototype = {
	
	_delay : null,
	_retry : null,
	_maxRetry : null,
	
	_init : function() {
		this._delay = 1000;
		this._retry = 0;
		this._maxRetry = 100;
	},
	
	call : function(func) {
		if (this._retry < this._maxRetry) {
			setTimeout(func, this._delay);
		}
		this._retry++;
	},
	
	setMaxRetryCount : function(no) {
		this._maxRetry = no;
	}
};

Application.MotifConflication = function() {
	this._init.apply(this, arguments);
};

$(document).ready(function() {
	new Application.genocon();
});

body {
    font-family: sans-serif;
    font-size: 14px;
}

a {
    color: #3B5998;
    font-weight: bold;
    text-decoration: none;
}

#gcAppContainer {
	width: 900px;
}

.hidden {
	display:none;
}

.left {
    float: left;
}

.label {
	color: #E87B10;
    font: 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    height: 24px;
    min-width: 165px;
}

input.baseSequence {
	/*width: 100%;*/
}

.highlight-sequence {
	font-weight: bold;
}

.resultArea {
    font-family: "Courier New","Lucida Console";
    margin: 10px 0;
    min-width: 410px;
    overflow: auto;
    width: 100%;
	background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
	white-space: nowrap;
}

.resultArea .userSequence {
	white-space: nowrap;
	float: left;
}

.finishSequence,
.replaceSequenc {
   background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    margin: 10px 0 0;
	font-family: "Courier New","Lucida Console";
	width: 100%;
	overflow: auto;
	white-space: nowrap;
}

.wrappedSequenceMotif {
	background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    margin: 10px 0 0;
	font-family: "Courier New","Lucida Console";
	overflow: auto;
	word-wrap: break-word;
	white-space: normal;
	width:100%;
	height:90px;
	word-break: break-all;
}

.replace {
    color: #E80010;
}

.baseErrorMessage,
.errorMessage {
	color: black;
	/*text-align: center;*/
	margin-bottom: -10px;
    margin-top: 10px;
}

.errorText {
	color: #FF0000;
}

.applicationContainer {
    background-color: #F6F6F6;
    border: 1px solid #CCCCCC;
    margin: 5px 0 0;
    padding: 5px;
}

.actionButtonContainer {
    text-align: right;
}

.actionBtn {
    border: 1px solid #DDDDDD;
    cursor: pointer;
    display: inline-block;
    font-weight: bold;
    padding: 5px 2px;
    text-align: center;
    width: 25px;
}

.row {
    padding: 5px 0;
}
.row:after {
    clear: left;
    content: "";
    display: block;
}
.row input[type="text"] {
    width: 200px;
}

.row .externalLink {
	margin: 0 5px;
}

.noborder {
    border: medium none;
}

#baseSequenceContainer .baseSequenceBox {
	width: 100%;
	overflow: auto;
	white-space: nowrap;
}
#baseSequenceContainer .baseSequenceBox span,
#baseSequenceContainer .baseSequenceBox .baseSequence {
	font-family: Courier;
}

#baseSequenceContainer .baseSequenceBox .fixedSequence {
	position: relative;
	left: -6px;
	color: #AAAAAA;
	font-weight: bold;
}

.applicationContainer .nextButtonContainer {
	margin-top: 10px;
}

.databaseInfo .motif {
	width: 70%;
}

/**
 * button css
 */

a.useButton {
	width: 150px;
}

.actionBtn {
	border: 1px solid #DDDDDD;
    cursor: pointer;
    display: inline-block;
    font-weight: bold;
    padding: 5px 2px;
    text-align: center;
    width: 25px;
}

.actionBtn:hover {
	border: 1px solid #000000;
}

.btn {
  display: inline-block;
  *display: inline;
  /* IE7 inline-block hack */

*zoom: 1;
  padding: 4px 10px 4px;
  margin-bottom: 0;
  font-size: 13px;
  line-height: 18px;
  color: #333333;
  text-align: center;
  text-shadow: 0 1px 1px rgba(255, 255, 255, 0.75);
  vertical-align: middle;
  background-color: #f5f5f5;
  background-image: -moz-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -ms-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));
  background-image: -webkit-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -o-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: linear-gradient(top, #ffffff, #e6e6e6);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);
  border-color: #e6e6e6 #e6e6e6 #bfbfbf;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
  border: 1px solid #cccccc;
  border-bottom-color: #b3b3b3;
  -webkit-border-radius: 4px;
  -moz-border-radius: 4px;
  border-radius: 4px;
  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  cursor: pointer;
  *margin-left: .3em;
}

.btn:hover,
.btn:active,
.btn.active,
.btn.disabled,
.btn[disabled] {
  background-color: #e6e6e6;
}

.btn:hover {
  color: #333333;
  text-decoration: none;
  background-color: #e6e6e6;
  background-position: 0 -15px;
  -webkit-transition: background-position 0.1s linear;
  -moz-transition: background-position 0.1s linear;
  -ms-transition: background-position 0.1s linear;
  -o-transition: background-position 0.1s linear;
  transition: background-position 0.1s linear;
}

.btn-blue,
.btn-blue:hover,
.btn-yellow,
.btn-yellow:hover,
.btn-red,
.btn-red:hover,
.btn-green,
.btn-green:hover,
.btn-lightblue,
.btn-lightblue:hover,
.btn-black,
.btn-black:hover {
  text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
  color: #ffffff;
}

.btn-blue {
  background-color: #0074cc;
  background-image: -moz-linear-gradient(top, #0088cc, #0055cc);
  background-image: -ms-linear-gradient(top, #0088cc, #0055cc);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0055cc));
  background-image: -webkit-linear-gradient(top, #0088cc, #0055cc);
  background-image: -o-linear-gradient(top, #0088cc, #0055cc);
  background-image: linear-gradient(top, #0088cc, #0055cc);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#0088cc', endColorstr='#0055cc', GradientType=0);
  border-color: #0055cc #0055cc #003580;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}

.btn-blue:hover,
.btn-blue:active,
.btn-blue.active,
.btn-blue.disabled,
.btn-blue[disabled] {
  background-color: #0055cc;
}

.btn-green {
  background-color: #5bb75b;
  background-image: -moz-linear-gradient(top, #62c462, #51a351);
  background-image: -ms-linear-gradient(top, #62c462, #51a351);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#51a351));
  background-image: -webkit-linear-gradient(top, #62c462, #51a351);
  background-image: -o-linear-gradient(top, #62c462, #51a351);
  background-image: linear-gradient(top, #62c462, #51a351);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#51a351', GradientType=0);
  border-color: #51a351 #51a351 #387038;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}
.btn-green:hover,
.btn-green:active,
.btn-green.active,
.btn-green.disabled,
.btn-green[disabled] {
  background-color: #51a351;
}
.btn-green:active,
.btn-green.active {
  background-color: #408140 ¥9;
}
.btn-lightblue {
  background-color: #49afcd;
  background-image: -moz-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -ms-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#2f96b4));
  background-image: -webkit-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -o-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: linear-gradient(top, #5bc0de, #2f96b4);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#2f96b4', GradientType=0);
  border-color: #2f96b4 #2f96b4 #1f6377;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}
.btn-lightblue:hover,
.btn-lightblue:active,
.btn-lightblue.active,
.btn-lightblue.disabled,
.btn-lightblue[disabled] {
  background-color: #2f96b4;
}

/* Dialog css */

.motifViewDialog .explanation {
	color: #AAAAAA;
	font-size: 12px;
	margin-left: 200px;
	margin-top : -10px;
}

.motifViewDialog .moreInfo {
	color: #3B5998;
	cursor: pointer;
}

.motifViewDialog .position {
	width: 70px;
}

.motifViewDialog .dialogErrorMessage {
	font-size: 12px;
}

.ui-corner-all, .ui-corner-top, .ui-corner-left, .ui-corner-tl {
    border-top-left-radius: 1px;
}
.ui-corner-all, .ui-corner-top, .ui-corner-right, .ui-corner-tr {
    border-top-right-radius: 1px;
}
.ui-corner-all, .ui-corner-bottom, .ui-corner-left, .ui-corner-bl {
    border-bottom-left-radius: 1px;
}
.ui-corner-all, .ui-corner-bottom, .ui-corner-right, .ui-corner-br {
    border-bottom-right-radius: 1px;
}

.loadingImageContainer .loadingMessage {
	color: #FF0000;
}

.motifConflictionDialog .option {
	margin: 10px;
}

.motifViewDialog {
	margin-top: 10px;	
}

.motifViewDialog .label {
	color: #E87B10;
    font: 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    height: 24px;
    width : 200px;
}

.motifViewDialog .motifviewinfo {
	float: right;
    margin-top: -150px;
    position: relative;
    width: 350px;	
}

.deletelink {
	cursor: pointer;	
}

.deletelink img {
	margin-bottom: -3px;	
}

.manualMotifView .manualMotifViewInfo {
	float: right;
    height: 90px;
    margin-right: 10px;
    margin-top: -65px;
    position: relative;
    width: 380px;
}

.baseSequenceBox textarea {
	resize: none;	
	width: 490px;
	height: 115px;
}

.fixedSequenceCheckBox {
	float: right;
    margin-right: 210px;
    margin-top: -115px;
}

.fixedSequenceMsg {
	float: right;
    margin-right: 20px;
    margin-top: -40px;
}

.fixedSequenceMotif {
	display: inline;
    float: right;
    font-family: "Courier New","Lucida Console";
    margin-top: -15px;
}

.resultAreaUserMessageClass {
	color: #0A5DA6;
    font: bold 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    font-size: 12px;
    font-weight: bold;
    margin-top: -6px;
	margin-bottom: 4px;
}

.finishSequence {
	 background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    font-family: "Courier New","Lucida Console";
    height: 100px;
    margin: 10px 0 0;
    overflow: auto;
    width: 480px;
    word-break: break-all;
    word-wrap: break-word;
	white-space: normal;
}

.finishSequenceFixed {
	/*display: inline;
    float: right;
    font-family: "Courier New","Lucida Console";
    margin-top: -15px;*/
	display: inline;
    float: left;
    font-family: "Courier New","Lucida Console";
    margin-left: 488px;
    margin-top: -30px;
    overflow: auto;
    width: 400px;
	word-wrap: break-word;
}

.manualsequence {
	float: right;
    height: 40px;
    overflow: auto;
    width: 300px;
	margin-bottom: 5px;
}

.motifviewsequence {
	float: right;
    height: 40px;
    margin-bottom: 5px;
    overflow: auto;
    width: 240px;
}

div.warningTop {
	background-color:#F6F6F6;
	font-weight:bold;
	color:#223194;
}

.error {
	color:#ED4A68;
}

.loadingChart .loadChartMessage {
	color:#FF0000;
}

.loadingChart {
	text-align: center;
}

.bottomChartTitle {
    color: #0A5DA6;
    font: bold 12px "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
}

.finishSequenceMsg {
	color: #0A5DA6;
    float: right;
    font: bold 13px "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    margin-top: -80px;
    width: 400px;
}

<div id="tests"> </div>
<div class="warningTop">Hover mouse over menu items for tooltip descriptions</div>
</br>
<div id="gcAppContainer">

<div id="baseSequenceContainer">
	<div class="label baseSequenceLabel">Base Sequence</div>
	<div class="baseSequenceBox">
		<span>
			<textarea type="text" cols=50 rows=5 class="baseSequence" value="" disabled=true maxlength=10000> </textarea>

		</span>
		



		<span class="fixedSequence">AGGTCTATATAAGCAGAGCTCTCTGGCTAAC</span>
		
		<div>
			<div class="fixedSequenceCheckBox"><input type="checkbox" id="chkEmptySequnce" value="true" checked=true>Start with empty sequence</div>
			<div class="fixedSequenceMsg">Minimal Promoter (fixed)</div>
		</div>
	</div>
	<div style="margin-top:5px;"><a class="useButton btn btn-green">Start promoter design</a></div>
	<div class="baseErrorMessage hidden"></div>
</div>
<div class="baseSequenceError hidden error">
	Warning: Motif contains nonstandard characters for DNA design. All characters except A, T, C, G will be treated as unique special characters. Currently IUPAC codes are not supported.
</div>
<div class="applicationContainer hidden">
	<div class="actionButtonContainer">
		<span class="appSummery"></span>
		<span class="collapseButton actionBtn" title="collapse">_</span>
		<span class="expandButton actionBtn" title="expand">+</span>
		<span class="removeButton actionBtn" title="remove">x</span>
		<br clear="all"/>
	</div>
	<div class="applicationDataContainer">
		
		<div class="row">
			<div class="label left optionListLabel">Select Tool</div>
			<div class="left">
				<select class="optionList"></select>
				
			</div>
		</div>

<div class="row hidden analysisMethodContainer">
			<div class="label left analysisMethodLabel">Analysis Method</div>
			<div class="left">
				<select class="analysisMethod"></select>
			</div>
		</div>
		
		<div class="row hidden expressionDbContainer">
			<div class="label left expressionDbLabel">Expression DataBase</div>
			<div class="left">
				<select class="expressionDb"></select>
			</div>
		</div>
		
		<div class="row hidden dataColContainer">
			<div class="label left dataColLabel">Data Collection</div>
			<div class="left">
				<select class="dataCol"></select>
			</div>
		</div>
		
		<div class="actionResultContainer"></div>
		<div class="nextButtonContainer hidden">
			<a class="btn nextButton">Next</a>
			<a class="btn repeatAgain">Repeat settings</a>
			<a class="btn finishNow">Finish Now</a>
		</div>
		<div class="finishSequenceContainer hidden">
			<div class="finishSequence"></div>

			<div class="finishSequenceMsg">Fixed minimal promoter sequence from -1 to -31 before the transcription start site, from CMV promoter.</div>
			<div class="finishSequenceFixed"></div>
		</div>
	</div>
</div>
</div>

Select Input Data

LinkData Work	Table Data
PEDB motif - Gene Atlas mashup table	PEDB_GeneAtlas_Brain_Neural_tissues PEDB_GeneAtlas_Dendritic_cells PEDB_GeneAtlas_Derived_cells PEDB_GeneAtlas_Digestive_system_organ PEDB_GeneAtlas_Endocrine_gland PEDB_GeneAtlas_Epidermis PEDB_GeneAtlas_Eye PEDB_GeneAtlas_Fibroblast PEDB_GeneAtlas_Gland PEDB_GeneAtlas_Heart_Muscle PEDB_GeneAtlas_Lymphocytes PEDB_GeneAtlas_Myeloid_leukocytes PEDB_GeneAtlas_Osteoblasts_Osteoclasts PEDB_GeneAtlas_Reproductive_organ PEDB_GeneAtlas_Respiration_organ PEDB_GeneAtlas_Spleen_Lymph_node PEDB_GeneAtlas_Stem_cells_Progenitors PEDB_GeneAtlas_Trunk_Abdomen_organ PEDB_GeneAtlas_White_Brown_adipose
Mammalian PromoterCAD Data Tables	PromoterCAD_Data_Tables
Mammalian PromoterCAD Plugins	PromoterCAD_plugins
Mammalian PromoterCAD Links	External_Links
Mammalian PromoterCAD Tool Tip	GeneAtlas_samples tooltip_DataTable tooltip_GeneAtlas tooltip_PromoterCAD_menus_buttons
Rank List of PEDB GeneAtlas	PEDB_GeneAtlas_all
Mouse promoter sequence	mouse_promoter_sequence

Add LinkData work(LinkData)

<h3>Tooltip</h3>

<p>
To facilitate the usability of PromoterCAD, we provide the tooltip informartion.
Then it is easy for users to undergo the promoter motif manipulation.
<br>
<br>
Hover the cursor to the items such as the button "Start promoter design",
and the PromoterCAD returns the messsage<br>
"Start your promoter design with the empty sequence in the region -32 to -10031 from the transcriptional start site."
<br>
<br>
Then users can start their promoter design by clicking the button.
</p>

</td>
<td>

</td>
</tr>
</tbody>
</table>

<h3>Basic Usage</h3>

<p>
To execute the synthetic promoter design using the PromoterCAD, please go through the following workflow basically.
</p>

<table>
<tbody>
<tr valign="top">
<td width="50%">

</td>
<td>

<ol>
<li>
At first, with the menu "Select tool", users can select one of the functions for performing
a particular data operation. For example, the function "MotifMaxExpress" finds
motifs associated with maximum gene expression in a specific condition.
Select this function to find motifs associated with strong expression in myeloid leukocyte samples.
</li>
<li>
With the menu "Analysis Method", users can select a regulatory motif data set (PEDB) registered in LinkData.
</li>
<li>
With the menu "Expression Database", users can select microarray expression database (Gene Atlas) registered in LinkData.
Data containing the sample conditions of mouse cell resources from Gene Atlas has been split into a series of data tables by tissue organ and cell types.
</li>
<li>
With the menu "Data Collection", users can select the data tables corresponding to the interesting sample condition.
(e.g. "Myeloid Leukocyte")
</li>
<li>
The next menu "Select Property", users can select one of the expression conditions
associated with the database. For the Gene Atlas data, this is represented by a
shorthand description. For example, "mast_cells_IgE" refers to a sample of mast cells,
stimulated with immunogloblin E (IgE). The gene expression is for mast cells.
<br>
The full description of each experiment can be referenced on the GEO website. For
example, these experiments are described here:<br>
<a target="_blank" href="
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM258713
">
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM258713
</a>
<br>
Select a particular experiment and MotifExpress will find known sequence
motifs associated with high expression in this condition. MotifMaxExpress will
automatically display these motif sequences (in this case septamers) in line with the
base promoter sequence at the same location as they occur in the promoter returned
by MotifExpress.
</li>
<li>
By clicking the button "Add motif", all the selected motifs are incorporated into the promoter motif skelton. The result will be displayed in the text area
 with the motifs indicated by color.
</li>
<li>
Click the button "Next", to repeat the sequence design operation and continue the
workflow. (Continues the steps 1-6.)
</li>
<li>
In the final step, click the button "Finish Now" to  fill in the skeleton (the 'bones' of the promoter, containing just regulatory motifs and the minimal promoter region) with the remaining sequence.
This will replace the blank '-' sequences, but will preserve any motifs added in the design process.
</li>
</ol>

</td>
</tr>
</tbody>
</table>

<h3>Tutorials</h3>

<p>
Here are tutorials to execute synthetic promoter designs using PromoterCAD. These have example walk throughs with snapshots for each step.
</p>
<table>

<tbody>
<tr valign="top">
<td>
<a target="_blank" href="https://hackpad.com/fvol30isGPL#PromoterCAD-Beginning-Tutorial-1">
Beginning_Tutorials_1
</a>
</td>
<td>
This tutorial illustrates how to design a synthetic promoter for Leaf specific expression using the MotifExpress tool.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/oNrS0K21sgd#PromoterCAD-Beginning-Tutorial-2:-Design-a-promoter-for-Circadian-expression-with-MotifCircadian">
Beginning_Tutorials_2
</a>
</td>
<td>
This tutorial illustrates how to design a synthetic promoter for Circadian expression with MotifCircadian tool.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/dAL1Omja3Mi#PromoterCAD-Beginning-Tutorial-3:-Use-InputMotif-to-add-specific-motifs-to-a-gene-design">
Beginning_Tutorials_3
</a>
</td>
<td>
This tutorial illustrates how to use InputMotif tool to add specific motifs to a gene design.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/4b72OO5mXOa#Advanced-Tutorial-1:-How-to-fork-your-own-PromoterCAD-workspace-and-make-workflow-snapshots">
Advanced_Tutorials_1
</a>
</td>
<td>
This tutorial illustrates how to fork your own PromoterCAD workspace.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/sxhIWdJ8Qix#Advanced-Tutorial-2A:-add-a-new-database-(normalized-data)-to-PromoterCAD">
Advanced_Tutorials_2A
</a>
</td>
<td>
This tutorial illustrates how to add a new normalized data to PromoterCAD.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/IWlEhmJ2jfT#Advanced-Tutorial-2B:-add-a-new-database-(PLACE-motif-data)-to-PromoterCAD">
Advanced_Tutorials_2B
</a>
</td>
<td>
This tutorial illustrates how to add a new database PLACE motif data to PromoterCAD.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/SLPqFU0AiLn#Advanced-Tutorial-3A:-Add-a-new-gene-expression-mining-plugin-to-PromoterCAD-(MotifRanking)">
Advanced_Tutorials_3A
</a>
</td>
<td>
This tutorial illustrates how to add a new data mining plugin tool MotifRanking.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/fzxSQrVTkdB#Advanced-Tutorial-3B:-Add-a-new-data-mining-plugin-to-PromoterCAD-(MotifNonCircadian)">
Advanced_Tutorials_3B
</a>
</td>
<td>
This tutorial illustrates how to add a new data mining plugin tool MotifNonCircadian.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/Advanced-Tutorial-4-cJ1VVvUtp1W">
Advanced_Tutorials_4
</a>
</td>
<td>
This tutorial illustrates how to modify and upload your own tooltips.
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/Help-Page-Interpreting-PromoterCAD-Output-VnHPootms0p">
Help Page
</a>
</td>
<td>
Interpreting PromoterCAD Output 
</td>
</tr>

<tr>
<td>
<a target="_blank" href="https://hackpad.com/Help-Page-How-to-tag-input-LinkData-tables-for-PromoterCAD-3WwOXIeohDL">
Help Page
</a>
</td>
<td>
How to tag input LinkData tables for PromoterCAD 
</td>
</tr>

</tbody>
</table>

<h3>License</h3>
<p>
PromoterCAD source code is licensed under  <a href="http://opensource.org/licenses/LGPL-3.0">the LGPL-3.0 license (the GNU Lesser General Public License, version 3.0)</a> and <a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">the Creative Commons license CC-BY-SA</a>.
So users can fork the source code of PromoterCAD to easily create their own data mining plugins. 
<br>
<a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">
<img src="http://app.linkdata.org/asset/8c72b4fc.png" width="20%">
</a>

</p>

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Description: <p> Mammalian PromoterCAD is an input data source extention of <a href="http://promotercad.org/">PromoterCAD</a>, which is a simple web-based UI for data-driven regulatory DNA design. Plugin tools are used to mine regulatory motifs from public databases, with an iterative design workflow for the accumulation of many motifs within a synthetic promoter design. The UI arbitrates when different introduced motifs overlap in position. </p> <br> Mammalian PromoterCAD web page:<br> <a href="http://promotercad.org/mammal/"> http://promotercad.org/mammal/ </a> <br> Manuals for PromoterCAD:<br> <a href="http://promotercad.org/manuals/"> http://promotercad.org/manuals/ </a> <br> <br> <strong> License </strong> <p> The source code for Mammalian PromoterCAD is now licensed under <a href="http://opensource.org/licenses/LGPL-3.0">the LGPL-3.0 license (the GNU Lesser General Public License, version 3.0)</a> and <a href="http://creativecommons.org/licenses/by-sa/3.0/deed.en">the Creative Commons license CC-BY-SA</a>, which allows for unlimited reuse and modification of the source code. Users can select either one of the licenses LGPL-3.0 and CC-BY-SA, when using the source code. Any users can access the source code of this application as follows. <br> <a href="http://app.linkdata.org/update/app1s449i"> http://app.linkdata.org/update/app1s449i</a> </p> Remove; Add description for another language