forked:GenoconApp｜Mash up the Linked Open Data

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

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

Application.genocon.prototype = {
	
	_baseSequence : null,
	
	_default : {
		baseSequenceContainerId : "baseSequenceContainer",
		baseErrorMessageClass : "baseErrorMessage",
		errorMessageEnterSequence : "Please enter a sequence of minimum length {0}",
		useButtonClass : "useButton",
		nextButtonClass : "nextButton",
		nextButtonContainerClass : "nextButtonContainer",
		collapseButton : "collapseButton",
		expandButton : "expandButton",
		removeButton : "removeButton",
		appContainerClass : "applicationContainer",
		appDataContainerClass : "applicationDataContainer",
		actionButtonContainer : "actionButtonContainer",
		actionResultContainer : "actionResultContainer",
		baseSequenceClass : "baseSequence",
		selectDataBaseList : "databaseList",
		selectMethodList : "optionList",
		hiddenBaseSequence : "hdnBaseSequence",
		databaseFilteringProperty : "#motif%20sequence",
		methodFilteringProperty : "#application%20URL",
		baseSequenceMinLength : 46
	},
	
	_init : function() {
		this._initDefaultContainer();
		this._initUseButtonListener();
	},
	
	_initDefaultContainer : function() {
		this._initDatabase();
		this._initMethod();
		this._initActionButton();
		this._initDatabaseListener();
		this._initMethodListener();
	},
	
	_initDatabase : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectDataBaseList);
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Database --</option>");
		$.each(LinkData.getFiles(), function(workId, fileNameList) {
			$.each(fileNameList, function(key, fileName) {
				var dbKey = self._getDatabaseOptionKey(workId, fileName);
				$.each(LinkData.getProperties(workId, fileName), function(pKey, pValue) {
					if (pValue.indexOf(self._default.databaseFilteringProperty) > 0) {
						$select.append("<option value='" + dbKey + "'>" + fileName + "</option>");
					}
				});
			});
		});
	},
	
	_initMethod : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Option --</option>");
		$.each(LinkData.getFiles(), function(workId, fileNameList) {
			$.each(fileNameList, function(key, fileName) {
				$.each(LinkData.getProperties(workId, fileName), function(pKey, pValue) {
					if (pValue.indexOf(self._default.methodFilteringProperty) > 0) {
						$.each(LinkData.getTriplesByProperty(workId, fileName, pValue), function(tKey, tValue) {
							var label = self._getLabel(tValue.subject);
							$select.append("<option value='" + tValue.object + "'>" + label + "</option>");
						});
					}
				});
			});
		});
	},
	
	_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() {
			$(this).closest("." + self._default.appContainerClass).remove();
		});
	},
	
	_initDatabaseListener : function() {
		var self = this;
		var $selectDb = $("." + self._default.appContainerClass + " ." + self._default.selectDataBaseList);
		$selectDb.change(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.selectMethodList + " option").removeAttr("selected");
			$container = $(parent).find("." + self._default.actionResultContainer);
			$container.html("");
		});
	},
	
	_initMethodListener : function() {
		var self = this;
		var $selectDb = $("." + self._default.appContainerClass + " ." + self._default.selectDataBaseList);
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$select.change(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$container = $(parent).find("." + self._default.actionResultContainer);
			$container.html("");
			var date = new Date();
			var id = "container_id_" + date.getTime();
			$container.attr("id", id);
			var method = $("option:selected", $(this)).text();
			var database = $("option:selected", $(parent).find("." + self._default.selectDataBaseList)).val();
			var func = function() {
				self._callback(self);
			}
			if (database != -1) {
				var arr = database.split("|");
				var obj = {
					workId : arr[0],
					fileName : arr[1],
					baseSequence : self._baseSequence,
					callback : func
				};
				eval(method)(id, obj);
			}
		});
	},
	
	_initUseButtonListener : function() {
		var self = this;
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.useButtonClass).click(function() {
			$txtSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass);
			self._baseSequence = $txtSeq.val();
			//$("#" + self._default.baseSequenceContainerId + " ." + self._default.hiddenBaseSequence).val($txtSeq.val());
			$errMsgEl = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseErrorMessageClass);
			$errMsgEl.hide();
			if (!self._baseSequence || self._baseSequence.length < self._default.baseSequenceMinLength) {
				$errMsgEl.html(self._default.errorMessageEnterSequence.replace("{0}", self._default.baseSequenceMinLength));
				$errMsgEl.show();
				//_showError($baseContainer, opts.msgEmptySequence);
			} else {
				$txtSeq.attr('readonly', true).addClass("noborder");
				$(this).hide();
				$("." + self._default.appContainerClass).show();
				//_appendAppContainer();
			}
		});
	},
	
	_callback : function(self) {
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonContainerClass).show();
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).click(function() {
			$parent = $(this).closest("." + self._default.appContainerClass);
			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();
			$parent.parent().append(clone);
		});
	},
	
	_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;
	}
	
};

$(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: 125px;
}

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;
	/*word-wrap: break-word;*/
}

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

.replaceSequence {
    background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    margin: 10px 0 0;
	font-family: "Courier New","Lucida Console";
	overflow: auto;
	/*word-wrap: break-word;*/
}

.replace {
    color: #E80010;
}

.baseErrorMessage,
.errorMessage {
	color: #FF0000;
	text-align: center;
}

.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;
}

.noborder {
    border: medium none;
}

/**
 * button css
 */

a.useButton {
	width: 80px;
}

.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;
}

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

#motifViewDialog .motifImageArea {
	height: 120px;
}

#motifViewDialog .position {
	width: 50px;
}

.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;
}

<div id="baseSequenceContainer">
	<div class="label">Base Sequence</div>
	<div>
		<input type="text" class="baseSequence" value="GTCAACATGGTGGAGCACGACACTCTCGTCTACTCCAAGAATATCAAAGATACAGTCTCAGAAGACCAGAGGGCTATTGAGACTTTTCAACAAAGTTAATGCGAGGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTCATCGAAAGGACAAGTGAAAGAGAAGATGGCTTCTACAAATGCCATCATTGCGATAAAGGAAAGGCTATCGTTCAAGATGCCTCTACCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAACATCTAGGGGAAAAAAGACGTTCCAACCACGTCTTCAAAGCAAGTGATTGGATTAAGGTTCTTCCACACGGTAAGGGATGGCACTAACACCTACCATCCTTCGCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGGACCTCGAC"/>
	</div>
	<div style="margin-top:5px;"><a class="useButton btn btn-green">Use</a></div>
	<div class="baseErrorMessage hidden"></div>
</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">Select Database</div>
			<div class="left"><select class="databaseList"></select></div>
		</div>
		<div class="row">
			<div class="label left">Select Option</div>
			<div class="left"><select class="optionList"></select></div>
		</div>
		<div class="actionResultContainer"></div>
		<div class="nextButtonContainer hidden"><a class="btn nextButton">Next</a></div>
	</div>
</div>
</div>
<div id="motifViewDialog" style="display:none">
	<input type="hidden" class="sequence"/>
	<div>
		<span>Place motif at position</span>
		<input type="text" class="position"/>
	</div>
	<div>
		<span class="explanation">Replace with prefer position between <span class="minSeq"></span> and <span class="maxSeq"></span></span>
	</div>
	<div class="motifImageArea">&nbsp;</div>
	<div>
		<span class="explanation">Click <a class="moreInfo">here</a> to see the additional information about motif from ATTEDII website</span>
	</div>
</div>

データ作品	テーブルデータ
GenoCon2 Challenge A - Developmental conditions 作者:GenoCon 更新日:2012年9月11日 5741 ダウンロード, 16 アプリケーション	Flowering Fruit_Seeds Leaf Root Seedling Stem Whole_Plant
GenoCon2 Challenge A - Developmental Coexpression (AtGenExpress + ATTED-II promoter motif) 作者:GenoCon 更新日:2012年9月19日 2662 ダウンロード, 7 アプリケーション Developmental Microarray Expression Data (AtGenExpress) of plant developmental tissues, combined with CEG coexpression analysis regulatory (7mer) motif calculations (ATTED-II). We took the median of triplicate measurements from AtGenExpress, then sorted the developmental series into plant tissues, with one category for seedlings (8 days old or less) and another for whole plants (older than 8 days). <br><br> <strong>References</strong> (for ATTED-II):<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17130150">http://www.ncbi.nlm.nih.gov/pubmed/17130150</a><br> <strong>References</strong> (for AtGenExpress)<br> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15806101">http://www.ncbi.nlm.nih.gov/pubmed/15806101</a>	Flowering_GeneExp_v3_median Fruit_Seeds_GeneExp_v3_median Heptamer_elements Leaf_GeneExp_v3_median Root_GeneExp_v3_median Seedling_GeneExp_v3_median Stem_GeneExp_v3_median Whole_Plant_GeneExp_v3_median
GenoCon2 Challenge A - Sequence Function Plugins 作者:GenoCon 更新日:2012年10月16日 1499 ダウンロード, 12 アプリケーション	Application_Plugins_for_Synthetic_Promoter_Design []