MzXml.as

package mz
{
	import flash.filesystem.File;
	import flash.filesystem.FileMode;
	import flash.filesystem.FileStream;
	import flash.utils.Dictionary;
	public class MzXml
	{
		/**
		 * A random access parser for mzXML files.  
		 * 
		 */		

		public var mz:Array;
		public var mzi:Array;
		
		private var f:File;
		private var fs:FileStream;
		private var fsize:int;
		private var index:Dictionary; // [[id, offset, length] , [id, offset,length],...]
		public function MzXml(file:File)
		{
			this.f = file;
			this.fs = new FileStream();
			
			// open the file to get the size
			fs.open(this.f,FileMode.READ);
			this.fsize = fs.bytesAvailable;
			fs.close()
			parseIndex();
		}

		private function parseIndex():void
		{
			this.index = new Dictionary;
		    // find index offset
			fs.open(f,FileMode.READ);
		    fs.position = new Number(fsize - 1000);
		    
		    var tmp:String = fs.readUTFBytes(fs.bytesAvailable);
		    //<indexOffset>33573953</indexOffset>
			var result:Array = tmp.match(/<indexOffset>(\d+)<\/indexOffset>/);
			var iof:Number = new Number(result[1]);
			
			// OK, now read in the index
			fs.position = iof;
			tmp = fs.readUTFBytes(fs.bytesAvailable);
			fs.close();
			// make a valid XML string to use by matching only the index structure 
			var xml:XML  = XML(tmp.match(/(<index>.+<\/index>)/m)[0]);
			// iterate through the index to get the offsets
			var i:int  = 0;
			for each (var offset:XML in xml.offset) {
				index[i] = [offset.@id, new int(offset.toString()),null];
				if (i > 0) {
					index[i-1][2] = index[i][1] - index[i-1][1];
				}
				i += 1;
			}
			// fix the last index length 
			index [i][2] = iof - index[i][1];
		}
	}
}