/* initializing the script */
window.onload = dtableInit;


function trim_Jvs(str)
{
	return str.replace(/^\s*|\s*$/,"");
}

function controle()
{
		var emailadress = document.getElementsByName("emailadress")[0].value

		if (emailadress.indexOf('@')==-1 || emailadress.indexOf('.')==-1)
		{
			return 0;
		}
		else
		{
			return 1;
		}
}


function generate_sugar()
{
	var variables = "generate.php?";

	// First, we check out and retrieve the extra-information
	variables += "water=" + document.getElementById("water").checked;
	if (trim_Jvs(document.getElementById("project_name").value)=='')
	{
		alert("Please enter a project name.");
		return;
	}
	else
	{
		variables += "&project_name=" + document.getElementById("project_name").value;
	}

	if (! controle())
	{
		alert("Please, enter a valid E-mail address.");
		return;
	}
	else
	{
		variables += "&email=" + document.getElementsByName("emailadress")[0].value;
	}

	// Second, we need the independant sugars and their associated patches
	var count_sugars = 0;
	var count_patch  = 0;
	var tbody_sugars = document.getElementById("sugar_table").childNodes[2];

	for (s=2; s<tbody_sugars.childNodes.length; s++)
	{
		if (tbody_sugars.childNodes[s].getAttribute("name")=="__SUGAR__")
		{
			var sug_nb = parseInt(trim_Jvs(tbody_sugars.childNodes[s].childNodes[0].childNodes[0].value));

			// Check whether the residue number is present
			if (isNaN(sug_nb))
			{
				alert("Please, enter a correct residue number (line " + (s-1).toString() + ").");
				return;
			}

			// Retrieving the sugars
			count_patch = 0;
			var op_sug  = tbody_sugars.childNodes[s].childNodes[1].childNodes[0];
			var sugar   = op_sug[op_sug.selectedIndex].value;
			var sugname = tbody_sugars.childNodes[s].childNodes[2].childNodes[0].value;
			variables  += "&sug_" + sug_nb + "_" + sugname + "=" + sugar_3L[sugar];

			// Recording the patches related to the previously retrieved saccharide
			var op_pat = tbody_sugars.childNodes[s].childNodes[3].childNodes[0];
			var patch  = op_pat[op_pat.selectedIndex].value;
			if (patch!="None")
			{
				variables += "&pat_" + sug_nb + "_" + count_patch + "=" + patch;
				count_patch++;
			}
			count_sugars++;
		}
		else
		{
			var op_pat = tbody_sugars.childNodes[s].childNodes[3].childNodes[0];
			var patch  = op_pat[op_pat.selectedIndex].value;
			if (patch!="None")
			{
				variables += "&pat_" + sug_nb + "_" + count_patch + "=" + patch;
				count_patch++;
			}
		}
	}


	// Finally, we retrieve the linkages
	var count_links = 0;
	var tbody_patches = document.getElementById("patch_table").childNodes[2];
	var phi_psi_OK   = false;
	for (s=2; s<tbody_patches.childNodes.length; s++)
	{
		var line         = tbody_patches.childNodes[s];



		if (line.childNodes[0].childNodes[0].getAttribute("name") == "nb1")		// Linkage
		{
			var opt_pat = line.childNodes[1].childNodes[0];
			var resi1   = parseInt(trim_Jvs(line.childNodes[0].childNodes[0].value));
			var resi2   = parseInt(trim_Jvs(line.childNodes[2].childNodes[0].value));
			var linkp   = opt_pat.options[opt_pat.selectedIndex].value;

			if (linkp!="None")		// A linkage type is specified
			{
				if (!(isNaN(resi1) || isNaN(resi2)))	// And two residues are specified
				{
					variables += "&link_" + count_links + "=" + resi1 + "_" + resi2 + "_" + linkp;
					count_links++;
					phi_psi_OK   = true;
				}
				else					// But at least one residue is not specified
				{
					alert("please, specify correct residues for the linkage " + eval(count_links+1));
					return;
				}

			}
			else if (!(isNaN(resi1) || isNaN(resi2)))	// No linkage type but 2 residues specified
			{
				alert("Please, specify a linkage type between residues " + resi1 + " and " + resi2);
				return;
			}
			else
			{
				phi_psi_OK   = false;
			}
		}
		else							// Phi and psi angle
		{
			if (phi_psi_OK)
			{
				var phi = parseFloat(trim_Jvs(line.childNodes[0].childNodes[0].value));
				var psi = parseFloat(trim_Jvs(line.childNodes[3].childNodes[0].value));

				if (! isNaN(phi)) variables += "&phi_" + count_links + "=" + phi;
				if (! isNaN(psi)) variables += "&psi_" + count_links + "=" + psi;
			}
		}
	}

	document.getElementById("generate_it").disabled = true;
	document.getElementById("show_info").innerHTML = '<IMG id="loading" src="Images/loading_green.gif" alt="Loading..." title="Loading..." width=200 height=200 border=0 hspace=0 vspace=0></IMG>';
	document.getElementById("tmp_calc").src = variables;
}


function pause(ms) 
{
	var date = new Date();
	var curDate = null;

	do
	{
		curDate = new Date();
	}
	while(curDate-date < ms);
}


function generate_simple(link)
{
	// Retrieving the name of the selected sugar
	var tr  = getParent(link.parentNode, "TR");
	var ind = tr.rowIndex;
	var opt = tr.childNodes[1].childNodes[0];
	var parameters = "generate_simple.php?name=" + sugar_3L[opt[opt.selectedIndex].value];

	// Some patches ?
	var count_patch = 0
	var opt = getParent(link, "TR").childNodes[3].childNodes[0];
	var pat = opt[opt.selectedIndex].value;
	if (pat != "None")
	{
		parameters += "&patch_" + count_patch + "=" + pat;
		count_patch++;
	}

	var tbody = getParent(link.parentNode, 'TBODY')

	if (tbody.rows.length > ind)
 	{
		for (s=ind; s<tbody.rows.length; s++)
		{
			if (tbody.rows[s].getAttribute("name")=="__PATCH__")
			{
				opt = tbody.rows[s].childNodes[3].childNodes[0];
				pat = opt[opt.selectedIndex].value;
				if (pat != "None")
				{
					parameters += "&patch_" + count_patch + "=" + pat;
					count_patch++;
				}
			}
			else
			{
				break;
			}
		}
	}

	TopJMol = findPosTop(tr) - 60;

	document.getElementById("show_sugar").style.cssText = "position:absolute; top:" + TopJMol.toString() + "px; left:" + LeftJMol.toString() + "px; border:0px solid black;";
	document.getElementById("show_sugar").innerHTML = '<IMG id="loading" src="Images/loading_red.gif" alt="Loading..." title="Loading..." width=200 height=200 border=0 hspace=0 vspace=0></IMG>';
	document.getElementById("tmp_calc").src = parameters;	// Running calculations in the hidden window
}


function getParent(element, parentTagName)
{
	/* Find the parent tag "parentTagName" of "element" */

	if ( ! element )
		return null;
	else if ( element.nodeType == 1 && element.tagName.toLowerCase() == parentTagName.toLowerCase() )
		return element;
	else
		return getParent(element.parentNode, parentTagName);
}


function findPosTop(obj)
{
	var curtop = 0;
	if(obj.offsetParent)
	{
		while(1)
		{
			curtop += obj.offsetTop;
			if(!obj.offsetParent) break;
			obj = obj.offsetParent;
		}
	}
	else
	{
		if(obj.y) curtop += obj.y;
	}
	return curtop;
}


function insertAfter(parent, node, referenceNode)
{
	parent.insertBefore(node, referenceNode.nextSibling);
}


function dtableInit()
{
	var table = document.getElementsByTagName('TABLE');
	var tbody = table[1].tBodies[0];
	var newSu = tbody.rows[0].cloneNode(true);
	tbody.rows[0].style.display = 'none';	// Hiding the reference sugar line
	tbody.rows[1].style.display = 'none';	// Hiding the reference patch line
	tbody.appendChild(newSu);


	// The same system for the patches table
	var tbody = table[2].tBodies[0];
	var newPa = tbody.rows[0].cloneNode(true);
	tbody.rows[0].style.display = 'none';
	tbody.rows[1].style.display = 'none';
	tbody.appendChild(newPa);

	// The first line cannot be removed
	document.getElementsByName("rem_button")[1].disabled = true;
	//document.getElementsByName("rem_linkage")[1].disabled = true;
	//document.getElementById("show_info").style.visibility = "hidden";
}


function addLine(link)
{
	/* Add a sugar */

	if (document.getElementsByName("rem_button").length == 2) document.getElementsByName("rem_button")[1].disabled = false
	
	// 1. Retrieving the "TABLE" node to manipulate
	var td = link.parentNode;
	var table = getParent(td,'TABLE');

	// 2. Manipulating the TBODY
	var tbody = table.tBodies[0];

	// 3. Cloning the reference line
	var newTr = tbody.rows[0].cloneNode(true);
	tbody.appendChild(newTr);
	
	if ( document.all )  // For IE
		newTr.style.display = "block";
	else
		newTr.style.display = "table-row"; // For Gecko
}


function delLine(link)
{
	/* Remove a sugar */

	if (document.getElementsByName("rem_button").length == 2) return;

	// 0. Deleting first all patches
	Remove_Patch_boxes(link)

	// 1. Removing the sugar
	var td = link.parentNode;
	getParent(td, 'TABLE').tBodies[0].removeChild(getParent(td, 'TR'));

	if (document.getElementsByName("rem_button").length == 2)
	{
		document.getElementsByName("rem_button")[1].disabled = true
	}
}


function Find_sugar_from_patch(link)
{
	var tbody = getParent(link.parentNode, 'TBODY')
	var rowi  = getParent(link.parentNode, 'TR').rowIndex
	for (row=rowi-1; row>1; row--)
	{
		if (tbody.childNodes[row].getAttribute("name")=="__SUGAR__")
		{
			break;
		}
	}

	var tr     = tbody.childNodes[row];
	var op_sug = tr.childNodes[1].childNodes[0];
	return op_sug.options[op_sug.selectedIndex].value;
}


function patch(link)
{
	/* Add or remove a patch */

	if (link.name == "patch")
	{
		var td = link.parentNode;
		var tr = getParent(td, 'TR');
		if (link.selectedIndex!="")
		{
			tr.childNodes[4].childNodes[0].removeAttribute('disabled')
		}
		else
		{
			var newatt = document.createAttribute("disabled");
			newatt.nodeValue = "true";
			tr.childNodes[4].childNodes[0].setAttributeNode(newatt);
		}
	}

	if (link.name == "patch_plus")
	{
		var which = getParent(link.parentNode, 'TR')
		var tbody = getParent(link.parentNode, 'TBODY')
		var newPa = tbody.rows[1].cloneNode(true);
		insertAfter(tbody, newPa, which);

		// Setting the correct patches for this sugar
		for (var i=newPa.childNodes[3].childNodes[0].options.length-1; i>=0; i--)
		{
			newPa.childNodes[3].childNodes[0].remove(i)
		}
		var sugar = Find_sugar_from_patch(link);
		newPa.childNodes[3].childNodes[0].options[0] = new Option("    ", value="None");
		newPa.childNodes[3].childNodes[0].options[0].selected = true;
		for (i in sugars[sugar])
		{
			newPa.childNodes[3].childNodes[0].options[newPa.childNodes[3].childNodes[0].options.length] = new Option(sugars[sugar][i], value=sugars[sugar][i])
		}

		if ( document.all )  // For IE
			newPa.style.display = "block";
		else
			newPa.style.display = "table-row"; // For Gecko
	}


	if (link.name == "patch_minus")
	{
		td = link.parentNode;
		if (getParent(td, 'TR').childNodes[0].hasChildNodes())	// Sugar line
		{
			getParent(link.parentNode, 'TR').childNodes[3].childNodes[0].selectedIndex = 0
			var newatt = document.createAttribute("disabled");
			newatt.nodeValue = "true";
			getParent(td, 'TR').childNodes[4].childNodes[0].setAttributeNode(newatt);			
		}
		else							// Patch line
		{
			getParent(link.parentNode, 'TBODY').removeChild(getParent(link.parentNode, 'TR'));
		}
	}

}


function Remove_Patch_boxes(link)
{
	var body = getParent(link.parentNode, 'TBODY')
	var line = getParent(link.parentNode, 'TR').rowIndex

	if (body.rows.length != line)
	{
		while (!body.childNodes[line].childNodes[0].hasChildNodes())
		{
			body.removeChild(body.childNodes[line])
			if (body.rows.length == line) break;
		}
	}
}


function ChangeSugar(link)
{
	Remove_Patch_boxes(link);

	var tr     = getParent(link.parentNode, "TR");
	var op_sug = tr.childNodes[1].childNodes[0];
	var op_pat = tr.childNodes[3].childNodes[0];
	var sugar  = op_sug.options[op_sug.selectedIndex].value;

	//for (var i=op_pat.options.length-1; i>=0; i--)
	//{
	//	op_pat.remove(i)
	//}

	while (op_pat.hasChildNodes())
	{
		op_pat.removeChild(op_pat.lastChild);
	}

	//for (var i=op_pat.optgroup.length-1; i>=0; i--)

	op_pat.options[0] = new Option("    ", value="None");
	for (var i in sugars[sugar])
	{
		if (sugars[sugar][i].split('')[0] == '*')
		{
			optGroup = document.createElement('optgroup');
			optGroup.label = sugars[sugar][i].replace(/\*/g, "").replace(/_/g, " ");
			op_pat.appendChild(optGroup);
		}
		else
		{
			op_pat.options[op_pat.options.length] = new Option(sugars[sugar][i], value=sugars[sugar][i]);
		}
	}

	// Disabling the plus button
	var newatt = document.createAttribute("disabled");
	newatt.nodeValue = "true";
	tr.childNodes[4].childNodes[0].setAttributeNode(newatt);			

	// Displaying the 3-letter name
	tr.childNodes[2].childNodes[0].value = sugar_3L[op_sug.value];
}


function CheckSugarName(link)
{
	var tr      = getParent(link.parentNode, "TR");
	var sugname = tr.childNodes[2].childNodes[0];
	var op_sug = tr.childNodes[1].childNodes[0];
	var sugar  = op_sug.options[op_sug.selectedIndex].value;

	if (sugname.value == "")
	{
		sugname.value = sugar_3L[sugar];
	}
}


function Linkage(link)
{
	if (link.name == "add_link")
	{
		// 1. Retrieving the "TABLE" node to manipulate
		var td = link.parentNode;
		var table = getParent(td,'TABLE');

		// 2. Manipulating the TBODY
		var tbody = table.tBodies[0];
		var newTr = tbody.rows[0].cloneNode(true);
		tbody.appendChild(newTr);

		if ( document.all )  // For IE
			newTr.style.display = "block";
		else
			newTr.style.display = "table-row"; // For Gecko
	}

	if (link.name == "rem_linkage")
	{
		// Checking first the presence of some phi/psi angles

		var ind = getParent(link.parentNode, 'TR').rowIndex;
		var tbody = getParent(link.parentNode, 'TBODY');
		if(tbody.childNodes.length>ind)
		{
			if(tbody.childNodes[ind].childNodes[0].childNodes[0].getAttribute("name") == "phi")
			{
				tbody.removeChild(tbody.childNodes[ind]);
				tbody.childNodes[ind-1].childNodes[4].childNodes[0].removeAttribute("disabled");
			}
		}

		if (document.getElementsByName("rem_linkage").length == 2)	// If only one line, we simply clear the field
		{
			tr = getParent(link.parentNode, 'TR');
			tr.childNodes[0].childNodes[0].value = '';
			tr.childNodes[2].childNodes[0].value = '';
			tr.childNodes[1].childNodes[0].selectedIndex = 0;
			
		}
		else								// Otherwise, we remove the line
		{
			getParent(link.parentNode, 'TBODY').removeChild(getParent(link.parentNode, 'TR'));
		}
	}

	if (link.name == "add_phipsi")
	{
		var which = getParent(link.parentNode, 'TR')
		var tbody = getParent(link.parentNode, 'TBODY')
		var newPa = tbody.rows[1].cloneNode(true);
		insertAfter(tbody, newPa, which);

		var newatt = document.createAttribute("disabled");
		newatt.nodeValue = "true";
		link.setAttributeNode(newatt);			

		if ( document.all )  // For IE
			newPa.style.display = "block";
		else
			newPa.style.display = "table-row"; // For Gecko
	}

	if (link.name == "rem_phipsi")
	{
		var ind = getParent(link.parentNode, 'TR').rowIndex - 2;
		var tbody = getParent(link.parentNode, 'TBODY');
		tbody.childNodes[ind].childNodes[4].childNodes[0].removeAttribute('disabled');
		tbody.removeChild(getParent(link.parentNode, 'TR'));
	}
}


document.write('<font color="black">');


var sugars   = new Array();var sugar_3L = new Array();