flykit.namespace("flykit.apps.byexpressionprofile");
flykit.apps.byexpressionprofile.CustomGeneFinderRenderer = function() {};
flykit.apps.byexpressionprofile.CustomGeneFinderRenderer.prototype = new flykit.genefinder.DefaultRenderer();
/**
* @private
* Render the results summary pane.
* @param {String} query the user's query
* @param {Number} count number of results found
*/
flykit.apps.byexpressionprofile.CustomGeneFinderRenderer.prototype._renderResultsSummary = function( query, count ) {
var _context = "flykit.genefinder.DefaultRenderer.prototype._renderResultsSummary";
try {
if (query instanceof Array) {
flykit.debug("found array query", _context);
query = query.join(", ");
}
var content = "found ";
content += count;
content += " matching D. melanogaster gene";
content += (count == 0 || count > 1) ? "s " : " ";
content += "from flybase.org ("+flykit.flybase.provenance+") ...";
this._resultsSummaryPane.innerHTML = content;
} catch (e) {
flykit.debug("caught "+e.name, ", "+e.message, _context);
throw new flykit.UnexpectedException(_context, e);
}
};
/**
* @class
* @constructor
*/
flykit.apps.byexpressionprofile.Application = function() {
var that = this;
var flyatlasprofile = null;
var genefinder = null;
var flyatlas = null;
var flyted = null;
var bdgp = null;
var flybasepub = null;
// var limit = 10000;
this.initQueryTable = function() {
/*
brain
*/
var content = "
";
for (var i=1;i";
}
content += "
";
/*for (var i=1;i";
}*/
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
content += "
";
$("#queryTableContainer").html(content);
}
this.initFlyatlasProfile = function() {
var context = "flykit.apps.byexpressionprofile.Application.initFlyatlasProfile";
try {
flykit.debug("instantiate a service for the flyatlas profile widget", context);
var service = new flykit.flyatlas.Service();
service.setEndpoint("../../../conf/flyatlas");
flykit.debug("instantiate a renderer for the batchgenefinder widget", context);
var renderPane = $("#flyatlasProfileWidget");
var renderer = new flykit.flyatlas.ProfileWidget.DefaultRenderer(); // default renderer
renderer.setCanvas(renderPane);
flykit.debug("instantiate a flyatlas profile widget", context);
flyatlasprofile = new flykit.flyatlas.ProfileWidget(service, renderer);
} catch (error) {
flykit.apps.byexpressionprofile.handleError(error);
}
}
this.initGeneFinder = function() {
try {
// initialise genefinder widget
flykit.info("instantiate a service for the genefinder widget");
var service = new flykit.flybase.Service("../../../conf/flybase");
flykit.info("instantiate a renderer for the genefinder widget");
var renderPane = document.getElementById("geneFinderWidget");
// var renderer = new flykit.genefinder.DefaultRenderer(); // default renderer
var renderer = new flykit.apps.byexpressionprofile.CustomGeneFinderRenderer();
renderer.setCanvas(renderPane);
flykit.info("instantiate a genefinder widget");
genefinder = new flykit.genefinder.Widget(service, renderer);
} catch (error) {
flykit.apps.byexpressionprofile.handleError(error);
}
};
this.initFlybasepub = function(){
try {
flykit.info("instantiate a service for the flybase publication widget");
var service = new flykit.flybasepub.Service();
service.setEndpoint("../../../conf/flybase");
flykit.info("instantiate a renderer for the flybase publication widget");
var renderer = new flykit.flybasepub.PublicationWidget.SimpleRenderer();
renderer.setCanvas($("#flybasepubPublicationWidget"));
flykit.info("instantiate a flybase publication widget");
flybasepub = new flykit.flybasepub.PublicationWidget(service, renderer);
} catch (error) {
flykit.apps.publicationmashup.handleError(error);
}
};
// called by this.init
this.initFlyatlas = function() {
try {
flykit.info("instantiate a service for the flyatlas widget");
var service = new flykit.flyatlas.Service();
service.setEndpoint("../../../conf/flyatlas");
flykit.info("instantiate a renderer for the flyatlas widget");
var renderer = new flykit.flyatlas.Widget.DefaultRenderer();
renderer.setCanvas($("#flyatlasWidget"));
flykit.info("instantiate a flyatlas widget");
flyatlas = new flykit.flyatlas.Widget(service, renderer);
} catch (error) {
flykit.apps.expressionmashup.handleError(error);
}
};
// called by this.init
this.initFlyted = function() {
try {
flykit.info("instantiate a service for the flyted image widget");
var service = new flykit.flyted.Service("../../../conf/flyted");
flykit.info("instantiate a renderer for the flyted image widget");
var renderPane = document.getElementById("flytedImageWidget");
// var renderer = new CustomFlytedRenderer();
var renderer = new flykit.flyted.ImageWidget.DefaultRenderer();
renderer.setCanvas(renderPane);
flykit.info("instantiate a flyted image widget");
flyted = new flykit.flyted.ImageWidget(service, renderer);
} catch (error) {
flykit.apps.expressionmashup.handleError(error);
}
};
// called by this.init
this.initBdgp = function() {
try {
flykit.info("instantiate a service for the bdgp image widget");
var service = new flykit.bdgp.Service("../../../conf/bdgp");
flykit.info("instantiate a renderer for the bdgp image widget");
var renderPane = document.getElementById("bdgpImageWidget");
// var renderer = new CustomBdgpRenderer();
// var renderer = new flykit.bdgp.ImageWidget.DefaultRenderer();
var renderer = new flykit.bdgp.ImageWidget.CompactRenderer();
renderer.setCanvas(renderPane);
flykit.info("instantiate a bdgp image widget");
bdgp = new flykit.bdgp.ImageWidget(service, renderer);
} catch (error) {
flykit.apps.expressionmashup.handleError(error);
}
};
this.init = function() {
var context = "flykit.apps.byexpressionprofile.Application.init";
try {
var logReader = new YAHOO.widget.LogReader("logger");
this.initQueryTable();
this.initFlyatlasProfile();
this.initGeneFinder();
this.initFlyatlas();
this.initFlyted();
this.initBdgp();
this.initFlybasepub();
flykit.debug("hook form submission to widget call", context);
YAHOO.util.Event.addListener("queryForm", "submit", this.onFormSubmitted);
flykit.debug("add listener for results received event", context);
flyatlasprofile.subscribe("RESULTSRECEIVED", this.onResultsReceived, null);
// attach gene selection listener to genefinder
genefinder.subscribe("GENESELECTED", this.onGeneSelected, null);
flykit.debug("application loaded, showing main pane", context);
$("#loadingPane").hide();
$("#applicationPane").show();
that.initState();
} catch (error) {
flykit.apps.byexpressionprofile.handleError(error);
}
};
this.onFormSubmitted = function(event) {
var context = "flykit.apps.byexpressionprofile.Application.onFormSubmitted";
try {
flykit.debug("form submitted", context);
var profile = {};
flykit.debug("build profile object", context);
for (var i=1;i 0) {
url = url.substring(0, term);
}
window.location.href = url + "#query=" + escape(statestring);
} catch (error) {
flykit.apps.byexpressionprofile.handleError(error);
}
};
this.initState = function() {
var context = "flykit.apps.byexpressionprofile.Application.initState";
try {
var url = new String(window.location.href);
var qi = url.indexOf("#query=");
if (qi > 0) {
var end = url.length;
var statestring = unescape(url.substring(qi+7,end));
flykit.info("found query: "+statestring);
var profile = {};
var params = statestring.split("|");
for (var i=0;i 0) {
profile[vals[0]] = vals[1];
var selectid = "select_"+vals[0]+"_change";
flykit.debug(selectid, context);
document.getElementById(selectid).value = vals[1];
}
}
var limit = document.getElementById("queryLimit").value;
that.doQuery(profile, limit);
}
} catch (error) {
flykit.apps.byexpressionprofile.handleError(error);
}
};
this.onResultsReceived = function(type, args) {
try {
flykit.debug("application: results received");
var results = args[0];
var flybaseids = results.genes;
genefinder.findGenesByAnyNameBatch(flybaseids);
$("#geneFinderWidget").show();
} catch (error) {
flykit.apps.byexpressionprofile.handleError(error);
}
};
this.onGeneSelected = function(type, args) {
try {
var gene = args[0];
flykit.info("gene selected: "+gene+" "+gene.flybaseID);
flyatlas.getAssaysByGene(gene);
flyted.findImagesByGene(gene);
bdgp.findImagesByGene(gene);
flybasepub.findPublicationsByGene(gene)
$("#flyatlasWidget").show();
$("#flytedImageWidget").show();
$("#bdgpImageWidget").show();
// that.setSelectionState(gene);
} catch (error) {
flykit.apps.expressionmashup.handleError(error);
}
};
this.init();
};
flykit.apps.byexpressionprofile.handleError = function(error) {
flykit.err(error.name+" :: "+error.message);
$("#errorMessage")
.html("an error has occurred, please see the log for more details")
.show();
};
// on dom ready, instantiate application
YAHOO.util.Event.onDOMReady(function() {new flykit.apps.byexpressionprofile.Application();});