// $Id$

var clickedMain;
var clickedPopUp;
var pathToImage = "/images/";

var group = -1;  // to indicate which group of sugars was chosen

var hoverN;
// may not need terminalArr
var terminalArr = new Array( 'TerminalbGlc', 'TerminalManB1','TerminalbGal','TerminalGlcNAcB1', 'TerminalaFuc','TerminalbFuc', 'TerminalbGlcAB', 'TerminalaManAB','TerminalbGalAB','TerminalbGlcNAcAB','TerminalaFucAB','TerminalbFucAB');
var action = -1;


var sq0 = new Square( -1, -1, 0, ''); // only sub is used
var sq1 = new Square( -1, -1, 0, '');
var sq2 = new Square( -1, -1, 0, '');
var sq3 = new Square( -1, -1, 0, '');
var sq4 = new Square( -1, -1, 0, '');
var sq5 = new Square( -1, -1, 0, '');
var sq6 = new Square( -1, -1, 0, '');
var sq7 = new Square( -1, -1, 0, '');
var sq8 = new Square( -1, -1, 0, '');
var sq9 = new Square( -1, -1, 0, '');
var sq10 = new Square( -1, -1, 0, '');
var sq11 = new Square( -1, -1, 0, '');
var sq12 = new Square( -1, -1, 0, '');

var squares = new Array( sq0, sq1, sq2, sq3, sq4, sq5, sq6, sq7, sq8, sq9, sq10, sq11, sq12);

var sugars = new Array();
sugars[0] = new Array('other');
sugars[1] = new Array('EndCH2CH2NH2', 'EndCH2CH2OH', 'EndOH'); // rightmost group
sugars[2] = new Array('2GlcpB1', '3GlcpB1', '4GlcpB1','6GlcpB1', 'Branch3,6GlcpB1', 'TerminalbGlc'); // glucose group
sugars[3] = new Array('2ManpB1','6DManpa1','TerminalManB1'); // mannose group
sugars[4] = new Array('2GalpB1', '6GalpB1', 'TerminalbGal'); // galactose group
sugars[5] = new Array ('2LRhapa1','TerminalLRhapa1','TerminalLRhapb1'); // rhamnose group
sugars[6] = new Array ('TerminalaFuc','TerminalbFuc'); // fucose group

sugars[7] = new Array('TerminalDGlcApb1'); //  glucuronic acid group
sugars[8] = new Array('TerminalManApa1'); // mannuronic acid group
sugars[9] = new Array('TerminalGalApb1'); // galacturonic acid group
sugars[10] = new Array('4GlcNAcpB1','TerminalGlcNAcB1'); // n-Acetyl-Glucosamine group
sugars[11] = new Array('TerminalDManNAcpa1'); // n-Acetyl-Mannosamine group

var branchedSugars = new Array();
branchedSugars[0] = new Array(); // for other
branchedSugars[1] = new Array(); // for rightmost group
branchedSugars[2] = new Array('2bGlc1AB','3bGlc1AB','4bGlc1AB','6bGlc1AB','TerminalbGlcAB'); //glucose group
branchedSugars[3] = new Array('2aMan1AB', '6aMan1AB','TerminalaManAB'); // mannose group
branchedSugars[4] = new Array('2bGal1AB','6bGal1AB','TerminalbGalAB'); // galactose group
branchedSugars[5] = new Array('2LRhapa1AB','TerminalaLRhaAB','TerminalbLRhaAB'); //  rhamnose group
branchedSugars[6] = new Array('TerminalaFucAB','TerminalbFucAB'); // fucose group

branchedSugars[7] = new Array('TerminalbGlcAAB'); // glucuronic acid group
branchedSugars[8] = new Array('TerminalaManA'); //  mannuronic acid group
branchedSugars[9] = new Array('TerminalbGalAAB'); // galacturonic acid group
branchedSugars[10] = new Array('4bGlcNAc1AB','TerminalbGlcNAcAB'); // n-Acetyl-Glucosamine group
branchedSugars[11] = new Array('TerminalaManNAcAB'); // n-Acetyl-Mannosamine group




function Square( group, sub, branched, src ){
	this.group = group;
	this.sub = sub;
	this.branched = branched;
	this.src = src;
}