function addBackground(background)
{
	if(background.checked)
	{
		//alert(background.value);
		var FM = document.frmManager;
		FM.Mode.value=background.value;
		FM.action=page+".jsp";
		FM.target="";
		FM.submit();
		return;

	}
}

function clearPaste()
{
	document.frmManager.pasteBox.value="";

}
function saveUploadHTML()
{
	clearPaste();
	document.frmManager.uploadHTML.value=document.getElementById("divUpload").innerHTML;
}
function saveManagerHTML()
{
	document.frmManager.managerHTML.value=document.getElementById("divManager").innerHTML;
}
function CLR(){
	document.frmManager.D1.length=0;
}

function RMV(){
	document.frmManager.D1.remove(document.frmManager.D1.selectedIndex);
}



function getFile(){
   if(document.frmManager.attach1.value !=""){
		document.frmManager.submit();
	}

}




function Clear(){
	document.frmManager.pasteBox.value="";
	document.frmManager.BOXVAL.value="";	
}

function getIDTName(){
	var FM = document.frmManager;
	FM.HIDTName.value = FM.Identifier.options[FM.Identifier.selectedIndex].text;
	FM.HIDT.value = FM.Identifier.options[FM.Identifier.selectedIndex].value;
}

function TextAreaPaster(){
	SendList();
}



function catchEnter(){
	return true;
}



function OpenHelp(part){
	var wnd = window.open("helps/functional_annotation.html#" + part, "Details", "width=600, height=350, toolbar=no, menubar=no, resizable=yes, scrollbars=yes");
	wnd.focus();
}

function OpenDemo(){
	parent.frames[2].document.location.href="Demo.jsp";
}
function showManager()
{
	
		saveUploadHTML();
		//document.getElementById("divUpload").innerHTML = "";
		//document.getElementById("divUpload").style.visibility = "hidden";
		document.getElementById("divUpload").style.height ="1";
		document.getElementById("divManager").innerHTML = document.frmManager.managerHTML.value;
		document.getElementById("divManager").style.visibility = "visible";
}
function showUpload()
{
	saveManagerHTML();
	//document.getElementById("divManager").style.visibility = "hidden";
	document.getElementById("divManager").style.height ="1";
	document.getElementById("divUpload").innerHTML = document.frmManager.uploadHTML.value;
	document.getElementById("divUpload").style.visibility = "visible";
}
function uploadList(page){
	//alert("start upload");
	var FM = document.frmManager;
	
	if(FM.Identifier.value ==""){
		alert("Please choose an identifier");
		return;
	}
	FM.idType.value=FM.Identifier.value;
	
	if(FM.rbUploadType[0].checked)
	{
		FM.uploadType.value=FM.rbUploadType[0].value;
	}
	else if(FM.rbUploadType[1].checked)
	{
		FM.uploadType.value=FM.rbUploadType[1].value;
	}
	else
	{
		alert("Error: Please specify whether this is a Gene list or a Background in step 3");
		return;
	}


	if(FM.fileBrowser.value !="")
	{
		FM.Mode.value="file";
		FM.action=page+".jsp";
		FM.target="";
		FM.submit();
		return;
	}

	if(FM.pasteBox.value == ""){
		alert("Error: Please either upload a file or paste a list in step 1.");
		return;
	}
	var ident=FM.Identifier.value;
	//alert("upload:"+ident);

	
		FM.Mode.value="paste";
		FM.ids.value=FM.pasteBox.value;
		FM.action=page+".jsp";
		FM.target="";
		FM.submit();

	}
function submitConvertedList(){
	alert("start converted upload");
		}

function refresh(page)
{
	//alert("refreshing");
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();
}

function useList(page)
{
	var FM = document.frmManager;
	FM.useIndex.value=FM.myLists.selectedIndex;
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();
}
function usePopList(page)
{
	var FM = document.frmManager;
	FM.usePopIndex.value=FM.popLists.options[FM.popLists.selectedIndex].value;
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();
}
function demoList(page,index)
{
	var FM = document.frmManager;
	FM.demoIndex.value=index;
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();
}

function removeList(page)
{
	var FM = document.frmManager;
	FM.removeIndex.value=FM.myLists.selectedIndex;
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();
}
function renameList(page)
{
	var FM = document.frmManager;
	FM.renameIndex.value=FM.myLists.selectedIndex;
	FM.newName.value=prompt("Enter a the new name for this list");

	FM.action=page+".jsp";
	FM.target="";
	FM.submit();
}
function renamePop(page)
{
	var FM = document.frmManager;
if(FM.popLists.options[FM.popLists.selectedIndex].value.indexOf('P')==0)
{
	FM.renamePopIndex.value=FM.popLists.selectedIndex;
	FM.newName.value=prompt("Enter a the new name for this list");

	FM.action=page+".jsp";
	FM.target="";
	FM.submit();

}
else
{
	alert('You can only rename an uploaded population.');
}
}


function combineList(page)
{
	var FM = document.frmManager;
	var listItems=FM.myLists.options;
	var combineIndexes=prompt("Enter a name for the combined list");

	//while(combineIndexes.length==0)
	//{
	//	combineIndexes=prompt("Enter a name for the combined list");

	//}
	var selCount=0;
	for(var c=0;c<listItems.length;c++)
	{
		if(listItems[c].selected==true)
		{
			combineIndexes=combineIndexes+","+c;
			selCount++;
		}
	}
	if(selCount<2)
	{
		alert("You must select at least 2 lists");
		return;
	}
//alert(combineIndexes);
	FM.combineIndex.value=combineIndexes;
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();

}
function combineBGList(page)
{
	var FM = document.frmManager;
	var listItems=FM.popLists.options;
	var combineBGIndexes=combineBGIndexes=prompt("Enter a name for the combined background");

	//while(combineBGIndexes.length==0)
	//{
	//	combineBGIndexes=prompt("Enter a name for the combined background");

	//}
	var selCount=0;
	for(var c=0;c<listItems.length;c++)
	{
		if(listItems[c].selected==true)
		{
			if(FM.popLists.options[FM.popLists.selectedIndex].value.indexOf('P')==0)
			{
				combineBGIndexes=combineBGIndexes+","+c;
				selCount++;
			}
			else
			{
				alert('You can only combine uploaded populations.');
				return;
			}
		}
	}
	if(selCount<2)
	{
		alert("You must select at least 2 backgrounds");
		return;
	}
//alert(combineBGIndexes);
	FM.combineBGIndex.value=combineBGIndexes;
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();

}
function selectSpecies(page)
{
	var FM = document.frmManager;
	var listItems=FM.speciesList.options;
	var selectedSpecies='';
	var selCount=0;
	if(listItems[0].selected==true)
	{
		for(var c=1;c<listItems.length;c++)
		{
			if(listItems[c].value.indexOf(':')>0)
			{
				selectedSpecies=selectedSpecies+","+listItems[c].value;
			}
		}

	}
	else
	{
		for(var c=1;c<listItems.length;c++)
		{
			if(listItems[c].selected==true)
			{
				if(listItems[c].value.indexOf(':')>0)
				{
					selectedSpecies=selectedSpecies+","+listItems[c].value;
				}

			}
		}
	}
	
//alert(selectedSpecies);
	FM.selectedSpecies.value=selectedSpecies;
	FM.action=page+".jsp";
	FM.target="";
	FM.submit();

}


function openUpload()
{
	var wnd =window.open("upload.jsp", "UploadWindow", "width=420, height=180, toolbar=no, menubar=no, resizable=yes, scrollbars=no");
	wnd.focus();
	return true;
}