basynthec-browser.js

// The width of the visualization
var w = 500;

var curveColors = d3.scale.category10().domain([0, 9]);

/**
 * Abstract superclass for the wrapper classes.
 * @constructor
 */
function AbstractThingWrapper() {
	this.isDataSet = function() { return false; }
	this.isStrain = function() { return false; }
}

/**
 * Create a wrapper on a data set designed to be displayed as a data set.
 * 
 * @constructor
 */
function DataSetWrapper(dataSet) {
	var strainNames;
	if (dataSet.properties[STRAIN_PROP_NAME] != null)
		strainNames = dataSet.properties[STRAIN_PROP_NAME].split(",");
	else
		strainNames = [dataSet.properties["STRAIN_NAME"]];
				
	this.strainNames = strainNames;
	this.dataSet = dataSet;
	this.dateString = timeformat(new Date(dataSet.registrationDetails.registrationDate));
	this.strainString = 
							(strainNames.length < 3) ?
								strainNames.join(" ") :
								"" + strainNames.length + " strain(s)";
	this.userEmail = dataSet.registrationDetails.userEmail;
	this.name = dataSet.code;
}

DataSetWrapper.prototype = new AbstractThingWrapper();
DataSetWrapper.prototype.constructor = DataSetWrapper;
DataSetWrapper.prototype.isDataSet = function() { return true; }

/**
 * Create a wrapper that represents a strain to be displayed
 *
 * @constructor
 */
function StrainWrapper(strainName)
{
	this.strainName = strainName;
	this.dataSets = [];
}

StrainWrapper.prototype = new AbstractThingWrapper();
StrainWrapper.prototype.constructor = StrainWrapper;
StrainWrapper.prototype.isStrain = function() { return true; }

var presenterModeTypeDataSet = "DATA_SET", presenterModeTypeStrain = "STRAIN";

/**
 * An object responsible for managing the view
 */ 
function AppPresenter() {
	this.didCreateVis = false;
	this.presenterMode = presenterModeTypeDataSet;
	this.visualizationContainers = [];
}

/** Hides the explanation and shows the element to display the explanation again */
AppPresenter.prototype.hideExplanation = function() {
	$('#explanation').hide();
	$('#explanation-show').show();	
}

/** Display the explanation again */
AppPresenter.prototype.showExplanation = function() {
	$('#explanation-show').hide();		
	$('#explanation').show();
}

/** Show the data sets grouped by type */
AppPresenter.prototype.switchToDataSetTypeView = function()
{
	this.presenterMode = presenterModeTypeDataSet;
	this.hideExplanation();
	this.toggleDisplayedVisualizations(dataSetTypeVis);
	od600InspectorView.removeAll(250);
	dataSetInspectorView.updateView();	
}

/** Show the data sets by strain*/
AppPresenter.prototype.switchToStrainView = function()
{
	this.presenterMode = presenterModeTypeDataSet;
	this.hideExplanation();
	this.toggleDisplayedVisualizations(strainVis);
	od600InspectorView.removeAll(250);	
	dataSetInspectorView.updateView();		
}

/** Show the data sets by strains with OD600 data*/
AppPresenter.prototype.switchToOD600View = function()
{
	this.presenterMode = presenterModeTypeStrain;
	this.hideExplanation();
	this.toggleDisplayedVisualizations(od600StrainVis);
	dataSetInspectorView.removeAll(250);
	od600InspectorView.updateView();
}

/** This view is very similar to the OD600 view, but the data is also divided into two main groups:
 * - strains for which there are phenotypes, predictions, and data in the openBIS database
 * - strains for which there are phenotypes or predictions, but no data in the openBIS database
 *   (in this group strains with phenotypes and predictions should be marked green; strains with 
 *   phenotypes only should be marked blue; strains with predictions only should be yellow) 
 * Information about the phenotypes and predictions is retrieved from UChicago strain database
 * (http://pubseed.theseed.org/model-prod/StrainServer.cgi) and cached at the server-side in OpenBIS.
 */
AppPresenter.prototype.switchToOD600WithPhenotypesAndPredictionsView = function()
{
	this.presenterMode = presenterModeTypeStrain;
	this.hideExplanation();
	this.toggleDisplayedVisualizations(od600StrainWithPhenotypesAndPredictionsVis);
	dataSetInspectorView.removeAll(250);
	od600InspectorView.updateView();
}

/** Utility function to gracefully switch from one visualization to another */
AppPresenter.prototype.toggleDisplayedVisualizations = function(visToShow)
{
	this.visualizationContainers.forEach(function(vis) {
		if (vis == visToShow) {
			if (od600StrainVis == vis || od600StrainWithPhenotypesAndPredictionsVis == vis) {
				// So that scrolling works
				vis.style("display", "block");
			} else {
				vis.style("display", "inline");
			}
			vis
				.transition()
			.duration(1000)
			.style("opacity", 1);
		} else {
			// change to "inline" element to eliminate jumping of two "block" elements during transition
			vis.style("display","inline");
			vis
				.transition()
			.duration(1000)
			.style("opacity", 0)
			.style("display", "none")
		}
	});
}

/**
 * Shows the list of data sets retrieved from the openBIS server.
 */
AppPresenter.prototype.showDataSets = function(bisDataSets) {
	if (null == bisDataSets) return;
	
	basynthec.dataSetList = bisDataSets.filter(function(dataSet) { 
		return IGNORED_DATASET_TYPES.indexOf(dataSet.dataSetTypeCode) == -1;
  });
	
	// sort data sets
	var sortByTypeAndRegistration = function(a, b) {
		if (a.dataSetTypeCode == b.dataSetTypeCode) {
			return b.registrationDetails.registrationDate - a.registrationDetails.registrationDate;
		}
		return (a.dataSetTypeCode < b.dataSetTypeCode) ? -1 : 1;
	};
	
	basynthec.dataSetList.sort(sortByTypeAndRegistration);

	model.initialize(function(){
		presenter.refreshDataSetTypeTables();
		presenter.refreshStrainTables();
		presenter.refreshOd600StrainTables();
		presenter.refreshOd600StrainWithPhenotypesAndPredictionsTables();
	});
}

AppPresenter.prototype.refreshStrainTables = function() {
  this.createVis();
 	strainView.updateView(1000);
}

AppPresenter.prototype.refreshDataSetTypeTables = function() {
  this.createVis();

	od600View.updateView();
	metabolomicsView.updateView();
	transcriptomicsView.updateView();
	proteomicsView.updateView();
	sequencesView.updateView();
}

AppPresenter.prototype.refreshOd600StrainTables = function() {
  this.createVis();
 	od600StrainView.updateView(1000);
}