function setSpecies(treeitem,gbrowse,blastdb){
	var species = collectElements('sp');
	for (i=0;i<species.length;i++){
			species[i].className = '';
		}
	treeitem.className = 'current';
	
	br = document.getElementById('browseLink');
	br.href = '/cgi-bin/gbrowse/'+gbrowse;
	bl = document.getElementById('blastLink');
	bl.href = 'search.php?show=blast&method='+blastdb;
	make_invisible('orgsearch_inactive');
	make_visible('orgsearch_active');
	}

function setOrg(select){
	var blastdb = select.value;
	
	bl = document.getElementById('blastLink');
	bl.href = 'search.php?show=blast&method='+blastdb;

	var gbrowse = blastdb.replace('_masked','');
	br = document.getElementById('browseLink');
	br.href = '/cgi-bin/gbrowse/'+gbrowse;
	
	}


function submitNodeSearch(type){
	nodeForm = document.getElementById('nodeSearch');
	for (var i = 0; i<nodeForm.elements.length;i++){
		switch (nodeForm.elements[i].name){
			case "method":
				if (nodeForm.elements[i].value == 'none'){
					window.alert('Please select a node');
					return false;
				}		
				else if (type=='blast' && nodeForm.elements[i].value == '0'){
					window.alert('You cannot BLAST against all nodes');
					return false;
				}
				break;
			case "show":
				nodeForm.elements[i].value = type;
				break;
		}
	}
	nodeForm.submit();
}

function setNode(node){
	nodeSelect = document.getElementById('nodeSelect');
	if (node == 'all'){
		makeGroupVisible('node');
		nodeSelect.value = '0';
		make_invisible('nodesearch_inactive');
		make_visible('nodesearch_active');
	}
	else{
		if (document.db == 'Metazome')
			var nodes = new Array('560','555','559','558','570','569','561','567','554');
		else if (document.db == 'Phytozome') var nodes = new Array('1088','1086','1084','1083','1081','1082','1085','1087','1089');

		makeGroupInvisible('node');
		make_visible('node_'+node);
		nodeSelect.value = nodes[node];
		make_invisible('nodesearch_inactive');
		make_visible('nodesearch_active');
	}
}

function checkLink(link){
	if (!link.href){
		window.alert('Please select an organism');
		return false;	
		}
	}


/* for new home page 7/29/2008 follows */

function selectNode(node){
	document.getElementById('treeOrgBox').className = 'noSelect';
	document.getElementById('treeNodeButtons').className = 'noSelect';
	document.getElementById('orgSelect').selectedIndex = 0;
	select = document.getElementById('nodeSelect');
	if (node==null){
		node = select.options[select.selectedIndex].value;
	}
	else{	
		//set the select box
		for(i=0;i<select.options.length;i++){
			if (select.options[i].value == node){
				select.selectedIndex = i;
			}
		}
	}
//	window.alert('you chose node '+node);
	box= document.getElementById('treeNodeBox');
	buttons= document.getElementById('treeNodeButtons');
	switch(node){
		case 'none':
			box.className='noSelect';
			make_invisible('allNodes');
			break;
		case '0':		
		case '1128':
		case '1129':
		case '1130':
		case '1131':
		case '1132':
		case '1133':
		case '1134':
		case '1135':
		case '1136':
		default:
			make_invisible('allNodes');
			box.className = 'box'+node;
			buttons.className = 'buttons'+node;
			break;
	}
}

function selectOrg(org){
	document.getElementById('treeNodeBox').className = 'noSelect';
	document.getElementById('treeNodeButtons').className = 'noSelect';
	document.getElementById('treeOrgOver').className = 'over_none';	
	document.getElementById('nodeSelect').selectedIndex = 0;
	select = document.getElementById('orgSelect');
	if (org==null){
		org = select.options[select.selectedIndex].value;
	}
	else{	
		//set the select box
		for(i=0;i<select.options.length;i++){
			if (select.options[i].value == org){
				select.selectedIndex = i;
			}
		}
	}	
	box= document.getElementById('treeOrgBox');
	switch(org){
		case 'none':
			box.className='noSelect';
			break;
		default:
			box.className=org;
			browse=document.getElementById('orgBrowseLink');
			browse.href = '/cgi-bin/gbrowse/'+org;
			blast=document.getElementById('orgBlastLink');
			blast.href ='search.php?show=blast&method='+org;
			break;
	}
}

function rollOverOrg(org){
	box= document.getElementById('treeOrgBox');
	if (box.className != org){
		document.getElementById('treeOrgOver').className = 'over_'+org;	
	}
}

function rollOverNode(node){
	box= document.getElementById('treeNodeBox');
	if (box.className != 'node'+node){
		document.getElementById('treeNodeDot').className = 'dot'+node;	
	}
}



/* january 21 2009 */

function selectOrg2(orgAlias){
	clearHomeBoxes();
	nodeSelect.selectedIndex = 0;
	select = document.getElementById('orgSelect');
	var found = 0;
	if (orgAlias==null){
		orgAlias = select.options[select.selectedIndex].value;
		found = 1;
	}
	else{	
		//set the select box
		for(i=0;i<select.options.length;i++){
			if (select.options[i].value == orgAlias){
				select.selectedIndex = i;
				found = 1;
			}
		}
	}	
	if(found){
		make_visible('box_'+orgAlias);
		box = dojo.byId('box_'+orgAlias);
		dojo.fadeIn({node:box}).play();
		selectList = document.getElementById('list_'+orgAlias);
		selectList.className = 'selected';
	}
}



function selectNode2(nodeAlias){
	clearHomeBoxes();
	orgSelect.selectedIndex = 0;
	select = document.getElementById('nodeSelect');
	var found = 0;
	if (nodeAlias==null){
		nodeAlias = select.options[select.selectedIndex].value;
		found = 1;
	}
	else{	
		//set the select box
		for(i=0;i<select.options.length;i++){
			if (select.options[i].value == nodeAlias){
				select.selectedIndex = i;
				found = 1;
			}
		}
	}	
	if(found) {
		make_visible('box_'+nodeAlias);
		box = dojo.byId('box_'+nodeAlias);
		dojo.fadeIn({node:box}).play();
		if(nodeAlias=='0') make_visible('allNodesSelect');
		else{
			selectDot = document.getElementById('nodeDotSelect');
			selectDot.className='select_'+nodeAlias
		}
	}
	else select.selectedIndex = 0;
}

/* january 5 2010 */

function selectOrg3(orgAlias){
	console.log('selectOrg');
	clearHomeBoxes();
	nodeSelect.selectedIndex = 0;
	select = document.getElementById('orgSelect');
	console.log('selectOrg a');
	var found = 0;
	if (orgAlias==null){
		console.log('selectOrg b');

		orgAlias = select.options[select.selectedIndex].value;
		found = 1;
	}
	else{	
		//set the select box
		for(i=0;i<select.options.length;i++){
			if (select.options[i].value == orgAlias){
				select.selectedIndex = i;
				found = 1;
			}
		}
	}	
	if(found){
		make_visible('box_'+orgAlias);
		box = dojo.byId('box_'+orgAlias);
		dojo.fadeIn({node:box}).play();
		selectList = document.getElementById('list_'+orgAlias);
		selectList.className = 'selected';
	}
	console.log('selectOrg done');
}



function selectNode3(nodeAlias){
	clearHomeBoxes();
	orgSelect.selectedIndex = 0;
	select = document.getElementById('nodeSelect');
	var found = 0;
	if (nodeAlias==null){
		nodeAlias = select.options[select.selectedIndex].value;
		found = 1;
	}
	else{	
		//set the select box
		for(i=0;i<select.options.length;i++){
			if (select.options[i].value == nodeAlias){
				select.selectedIndex = i;
				found = 1;
			}
		}
	}	
	if(found) {
		make_visible('box_'+nodeAlias);
		box = dojo.byId('box_'+nodeAlias);
		dojo.fadeIn({node:box}).play();
		if(nodeAlias=='0') make_visible('allNodesSelect');
		else{
			selectDot = document.getElementById('nodeDotSelect');
			selectDot.className='select_'+nodeAlias
		}
	}
	else select.selectedIndex = 0;
}




function nDot(x,y){
	x=x+278;
	y=y+73;
	dot = document.getElementById('nodeDot');
	dot.style.display = '';
	dot.style.left = x+'px';
	dot.style.top = y+'px';
}

function urHere(text){
	if(text==null) text='';
	urhBox = document.getElementById('cursorBox');
	urhBox.innerHTML = text;

}


function clearHomeBoxes(){
	selectDot = document.getElementById('nodeDotSelect');
	selectDot.className = 'select_None';
	make_invisible('allNodesSelect');
	orgSelect = document.getElementById('orgSelect');
	for (var i = 0; i<orgSelect.options.length;i++){
		var box = dojo.byId('box_'+orgSelect.options[i].value);
		if(box) { 
			dojo.fadeOut({node:box}).play();
			make_invisible('box_'+orgSelect.options[i].value);
		}
	}
	list = document.getElementById('homepageOrgs');
	for (var i = 0; i<list.childNodes.length;i++){
		list.childNodes[i].className='';
	}	
	
	nodeSelect = document.getElementById('nodeSelect');
	for (var i = 0; i<nodeSelect.options.length;i++){
		var box = dojo.byId('box_'+nodeSelect.options[i].value);
		if(box){
			dojo.fadeOut({node:box}).play();
			make_invisible('box_'+nodeSelect.options[i].value);
		}
	}
}



function labelFadeIn(id){
	label= dojo.byId(id);
	dojo.fadeIn({node:label}).play();
}

function labelFadeOut(id){
	label= dojo.byId(id);
	dojo.fadeOut({node:label}).play();
}