function highlight_mirna(org, allorg,id,start, end){
var organisms = new Array();
organisms = org.split(';');
var allOrganisms =  allorg.split(';');
for (i = 0; i < allOrganisms.length; i++){
org = allOrganisms[i];
obj = document.getElementById(org);
cleanstring = obj.innerHTML.replace(/<span class=highlight id=MIRNA>/i,"");//first replace is for IE, thanks MS
cleanstring1 = cleanstring.replace(/<span id=\"MIRNA\" class=\"highlight\">/i,"");
cleanstring2 = cleanstring1.replace(/<\/span>/i,"");
obj.innerHTML = cleanstring2.substring(0);
}

for (i = 0; i < organisms.length; i++){
org = organisms[i];
obj = document.getElementById(org);
cleanstring = obj.innerHTML.replace(/<span class=highlight id=MIRNA>/i,"");//first replace is for IE, thanks MS
cleanstring1 = cleanstring.replace(/<span id=\"MIRNA\" class=\"highlight\">/i,"");
cleanstring2 = cleanstring1.replace(/<\/span>/i,"");
obj.innerHTML = cleanstring2.substring(0,start-1) + "<span id=\"MIRNA\" class=\"highlight\">" + cleanstring2.substring(start-1,end) + "</span>" + cleanstring2.substring(end);
}
s = "";
n = start;
while (--n >= 0) 
s += "&nbsp;";

annotationstring = s + id;
obj2 = document.getElementById("idtrack");
obj2.innerHTML = annotationstring;
obj3 = document.getElementById('MIRNA');
var scrollregion=document.getElementById("msa_alignment");
scrollregion.scrollLeft = obj3.offsetLeft-320;

//bj3.scrollIntoView(false);
//obj3.scrollIntoView(false);//needed to repeat, otherwise strange behavior

}

//function reset(){
 //if(document.getElementsByTagName){  
   //var table = document.getElementById(id);  
//   obj = document.getElementsByName(org);
 //  obj.innerHTML = "";
//}
function alternate(id){

 if(document.getElementsByTagName){  
 if(document.getElementById(id)){
   var table = document.getElementById(id);  
   var rows = table.getElementsByTagName("tr");  
   j=0;
   for(i = 0; i < rows.length; i++){          
 //manipulate rows
     
	if(rows[i].className == "invisible"){
	}
	else{
	j++;
	if(j % 2 == 0){
       rows[i].className = "even";
     }else{
       rows[i].className = "odd";
     }      
   }
   }
 }
 }
}

function draw_box(groupcoords,X1,Y1,X2,Y2){
jg.clear();
var x1offset = 0;
var y1offset = 7;
var x2offset = 0;
var y2offset = 7;
if(navigator.appName == "Netscape")
{
 x1offset = 7;
 y1offset = 7;
 x2offset = 7;
 y2offset = 7;
}
 if(navigator.appName == "Microsoft Internet Explorer")
{
 x1offset = -5;
 y1offset = 7;
 x2offset = 10;
 y2offset = 7;
}
var eachbox = new Array();
eachbox = groupcoords.split(';');
for (i = 0; i < eachbox.length; i++){
var coords = new Array();
coords = eachbox[i].split(',');
if(coords.length == 4){
x1 = parseInt(coords[0]);
y1 = parseInt(coords[1]);
x2 = parseInt(coords[2]);
y2 = parseInt(coords[3]);
jg.drawRect(x1+x1offset,y1+y1offset,x2-x1+x2offset,y2-y1+y2offset);
}
}
if(X1){
jg.setStroke(2);
X1 = parseInt(X1);
Y1 = parseInt(Y1);
X2 = parseInt(X2);
Y2 = parseInt(Y2);
jg.drawRect(X1+x1offset,Y1+y1offset,X2-X1+x2offset,Y2-Y1+y2offset);
}
jg.paint();
jg.setStroke(1);
}

function show_famRNA(table1,table2,miRNA){
if(document.getElementById(table1)){
var table = document.getElementById(table1)
var rows = table.getElementsByTagName("tr");
//alert(miRNA);
for(i = 0; i < rows.length; i++){          
 //manipulate rows
 rows[i].className = "";
     if(rows[i].getAttribute("name") == miRNA){
       rows[i].className = "";
     }
	else if(rows[i].getAttribute("name") != "header"){
       //alert(rows[i].Name);
	  rows[i].className = "invisible";
     }
             
   }
   alternate(table1);
   }
  if(document.getElementById(table2)){
var table = document.getElementById(table2)
var rows = table.getElementsByTagName("tr");
//alert(miRNA);
for(i = 0; i < rows.length; i++){          
 //manipulate rows
 rows[i].className = "";
     if(rows[i].getAttribute("name") == miRNA){
       //alert(miRNA);
	  //alert("test");
	  rows[i].className = "";
     }
	else if(rows[i].getAttribute("name") != "header"){
       //alert(rows[i].Name);
	  rows[i].className = "invisible";
     }
             
   }

alternate(table2);
}
}
function hide_column(tablename,colnames){
var table = document.getElementById(tablename)
var headers = table.getElementsByTagName("th");
var cells = table.getElementsByTagName("td");
//alert(miRNA);
var eachcol = new Array();
eachcol = colnames.split(';');
for(i = 0; i < headers.length; i++){          
 //manipulate rows headers[i].className = "";
 if(headers[i].getAttribute("name") == eachcol[0]){
       headers[i].className = "invisible";
     }
}
for(i = 0; i < cells.length; i++){          
 //manipulate rows cells[i].className = "";
 for (j = 1; j <= eachcol.length; j++){

     if(cells[i].getAttribute("name") == eachcol[j]){
       cells[i].className = "invisible";
     }
	}   
   }

}

function reset_hiddencolumns(tablename){
var table = document.getElementById(tablename)
var headers = table.getElementsByTagName("th");
var cells = table.getElementsByTagName("td");
for(i = 0; i < headers.length; i++){          
headers[i].className = "";
}
for(i = 0; i < cells.length; i++){          
 cells[i].className = "";
}

}