<?xml version="1.0" encoding="utf-8"?>
<mx:Application 
viewSourceURL="@mx-springgraph-sample-MoleculeViewer.html" xmlns:mx="http://www.adobe.com/2006/mxml" xmlns:flex="http://www.adobe.com/2006/fc" xmlns="*" xmlns:molecules="molecules.*" 
	layout="absolute" creationComplete="startup()" 
	>
	
	<!--
	////////////////////////////////////////////////////////////////////////////////
	//
	//  Copyright (C) 2006 Adobe Macromedia Software LLC and its licensors.
	//  All Rights Reserved. The following is Source Code and is subject to all
	//  restrictions on such code as contained in the End User License Agreement
	//  accompanying this product.
	//
	////////////////////////////////////////////////////////////////////////////////
	-->
	
	<!-- This application display schematic layouts of various molecules. 
		The molecule definitions are fetched from XML files that use the 
		CML markup language to define molecules as atoms and bonds. 
		For more info on CML, see http://www.xml-cml.org/.
		
		This app was written in Flex 2, using FlexBuilder. Most of the work
		is done by the SpringGraph component.
		
		Written by Mark Shepherd, Nov 2006
	-->

	<!-- The UI -->
	
	<!-- the springgraph covers the entire area -->
	<flex:SpringGraph id="springgraph" bottom="0" top="0" right="0" left="0" backgroundColor="#666666" 
		repulsionFactor="{repulsion.value}" dataProvider="{graph}" itemRenderer="springgraph_sample_MoleculeViewer_AtomView"/>
		
	<!-- various controls appear superimposed over the springgraph -->
	<mx:Label x="10" y="69" fontSize="16" fontFamily="Verdana" color="#dddddd" id="moleculeTitle"/>
	<mx:HSlider x="10" y="13" width="114" id="repulsion" value="0.60" minimum="0.0" maximum="1.5" liveDragging="true"/>
	<mx:HSlider x="10" y="39" width="114" id="scaleSlider" value="0.43" minimum="0.1" maximum="2.0" liveDragging="true"
		change="this.scaleFactor = scaleSlider.value"/>
	<mx:List id="moleculeList" width="114" backgroundAlpha="0.2" color="0xffffff"
		dataProvider="{moleculeNames}" selectedIndex="0"
		change="loadCMLFile((event.currentTarget as List).selectedItem as String)"
		rollOverColor="0xcccccc" selectionColor="0xdddddd" bottom="57" left="10" top="101"/>
	<mx:Label text="about" fontSize="14" click="doAbout()" bottom="27" height="23" left="44"
		color="#dddddd" 
		rollOver="event.currentTarget.setStyle('color', 0xffffff)" 
		rollOut="event.currentTarget.setStyle('color', 0xdddddd)"/>
	<mx:Text fontSize="9" color="#dddddd" textAlign="center" width="114"
		htmlText="&lt;a href=&quot;http://mark-shepherd.com&quot;&gt;mark-shepherd.com&lt;/a&gt;" bottom="10" left="10"/>

	<!-- The Scripts -->

	<mx:Script>
		<![CDATA[
			import mx.managers.PopUpManager;
			import mx.core.IFlexDisplayObject;
			import com.adobe.flex.extras.controls.springgraph.Item;
			import com.adobe.flex.extras.controls.springgraph.Graph;
			
			/** this function runs when all the components have been fully created. We load in 
			    our first data file, using whatever is the default selection in moleculeList. */
			private function startup(): void {
				loadCMLFile(moleculeList.selectedItem as String);
			}

			/** Initiates the fetch of a CML file. When the file has finished loading,
				it will be processed in the gotData function. */
			private function loadCMLFile(file: String): void {
				cmlService.url = 'springgraph-sample-MoleculeViewer-cmlfiles-' + file + '.xml';


				cmlService.send();
			}
				
			[Bindable]
			/** the current scale factor applied to all AtomView's. There is a slider
			    in the UI that controls this. (Note: I chose a smallish default value 0.43 because
			    the performance seems to be better. I think this performance difference
			    is not because the drawing is faster, but rather because the SpringGraph
			    is able to find a stable layout in fewer iterations). */
			public var scaleFactor: Number = 0.43;
				
			[Bindable]
			/** the graph that provides the item/link (a.k.a atom/bond) data
			    to the SpringGraph. */
			public var graph: Graph = new Graph();

			public static function getInstance(): springgraph_sample_MoleculeViewer {
				return Application.application as springgraph_sample_MoleculeViewer;
			}
			
			/** called when the fetch of a CML file has successfully completed. */
			private function gotData(event: Event): void {
				// throw away the molecule we are currently viewing.
				// BTW, if you don't do this, it works fine, you get several molecules on 
				// the display at same time. The only problem is that the SpringGraph
				// starts to get slow.
				graph.empty();
				
				// load the CML data into the graph
				loadCML(event.currentTarget.lastResult, graph);			
				
				// set the title that appears in the UI
				moleculeTitle.text = event.currentTarget.lastResult.@title;
			}
			
			// This namespace is used in some, but not all, CML files
			public static var cmlns:Namespace = new Namespace("x-schema:cml_schema_ie_02.xml");
			
			/** loads a CML document into a Graph. We only use the <atom> and <bond> tags,
			and ignore all the other information and tags in the CML. */
			private static function loadCML(cml: XML, g: Graph): void {
				var gid: String = cml.@id;
				var item: Item;
				
				// look for <atom> elements that have no namespace
				for each (var node: XML in cml..atom) {
					item = new Item(gid + node.@id);
					item.data = node;
					g.add(item);
				}
				
				// look for <atom> elements in the standard CML namespace
				for each (node in cml..cmlns::atom) {
					item = new Item(gid + node.@id);
					item.data = node;
					g.add(item);
				}
				
				// look for <bond> elements that have no namespace
				for each (var bond: XML in cml..bond) {
					loadBond(bond, g, gid);
				}
				
				// look for <bond> elements in the standard CML namespace
				for each (bond in cml..cmlns::bond) {
					loadBond(bond, g, gid);
				}
			}
			
			/** load a bond into a graph. A bond looks like this
			 *   <bond id="b6">
     	 	 *		<string builtin="atomRef">a6</string>
   			 *		<string builtin="atomRef">a7</string>
  			 *		<string builtin="order">1</string>
 			 *   </bond>
			 */
			private static function loadBond(bond: XML, g: Graph, gid: String): void {
				var fromID: String;
				var toID: String;
				var orderString: String;
				
				try {
					// try finding the info without using a namespace
					fromID = bond.string[0].toString();
					toID = bond.string[1].toString();
					orderString = bond.string.(@builtin == "order");
				} catch (e: Error) {
					// that failed. try again using a namespace.
					fromID = bond.cmlns::string[0].toString();
					toID = bond.cmlns::string[1].toString();
					orderString = bond.cmlns::string[2].toString(); //.(@builtin == "order");
				}
				
				// find the 2 atoms, based on their id's
				var fromItem: Item = g.find(gid + fromID);
				var toItem: Item = g.find(gid + toID);
				
				if((fromItem != null) && (toItem != null)) {
					// get the 'order' of the bond. Make sure it's a sensible number.
					var order: int = int(orderString.toString());
					if(order < 0) order = 0;
					if(order > 10) order = 10;
					
					// create the data object that is associated with this edge.
					// this object must specify various visual parameters for the line
					// that represents the bond. (note: its ok to omit this, in
					// which case the edge will be drawn using default settings).
					var data: Object = {settings: {alpha: 0.5, color: 0, thickness: (order * 3) - 2}};
					
					// add the bond (a.k.a. link) to the graph
					g.link(fromItem, toItem, data);
				}
				// todo: the bind information sometimes has a 'stereo' value with values like H and W. do something with this.
			}

			/** pops up the about box */
			private function doAbout(): void {
				var aboutWindow: IFlexDisplayObject = new springgraph_sample_MoleculeViewer_AboutWindow();
				PopUpManager.addPopUp(aboutWindow, this, true);		
				PopUpManager.centerPopUp(aboutWindow);		
			}
		]]>
	</mx:Script>

	<!-- The data -->
	
	<!-- a component that we use to send http requests to get the cml data files. -->
	<mx:HTTPService id="cmlService" showBusyCursor="true" resultFormat="e4x" result="gotData(event)"/>
	
	<!-- A list of the CML data files we use. These data files are stored along with the MoleculeViewer application,
	     (in the cmlfiles folder), so that they can be fetched without violating the Flash sandbox rules. 
	     The files originally come from http://www.xml-cml.org/, to whom I am very grateful. There are lots
	     more files there if you want to play with them, but beware - the big ones are slow -->
	<mx:Array id="moleculeNames">
		<mx:String>accholine</mx:String>
		<mx:String>adenosine</mx:String>
		<mx:String>adrenalin</mx:String>
		<mx:String>aminopval</mx:String>
		<mx:String>baclofen</mx:String>
		<mx:String>bicuculli</mx:String>
		<mx:String>bufotenin</mx:String>
		<mx:String>carotine</mx:String>
		<mx:String>choline</mx:String>
		<mx:String>clozapine</mx:String>
		<mx:String>diazepam</mx:String>
		<mx:String>dopamine</mx:String>
		<mx:String>glutamate</mx:String>
		<mx:String>histamine</mx:String>
		<mx:String>indoleace</mx:String>
		<mx:String>kainate</mx:String>
		<mx:String>naloxone</mx:String>
		<mx:String>nicotine</mx:String>
		<mx:String>riboflavin</mx:String>
		<mx:String>serotonin</mx:String>
		<mx:String>tyrosine</mx:String>
	</mx:Array>
	
</mx:Application>