function change_checkbox_state(elements_count, control_prefix, state_control_name) {
	var state_control = document.getElementById(state_control_name);
	for (i = 0; i < elements_count; i++) {
		control_checkbox_name = control_prefix + "[" + i + "]";
		control_checkbox = document.getElementById(control_checkbox_name);
		if(control_checkbox != null) {
			control_checkbox.checked = state_control.checked;
		}
	}
}

/**
 * This array is used to remember mark status of rows in browse mode
 */
var marked_row = new Array;

/**
 * Sets/unsets the pointer and marker in browse mode
 *
 * @param   object    the table row
 * @param   integer  the row number
 * @param   string    the action calling this script (over, out or click)
 * @param   string    the default background color
 * @param   string    the color to use for mouseover
 * @param   string    the color to use for marking a row
 *
 * @return  boolean  whether pointer is set or not
 */
function setPointer(theRow, theRowNum, theAction)
{
    var theDefaultColor = '#FFFFFF';
    var thePointerColor = '#CCFFCC';
    var theMarkColor = '#FFCC99';
    var theCells = null;

    // 1. Pointer and mark feature are disabled or the browser can't get the
    //    row -> exits
    if ((thePointerColor == '' && theMarkColor == '')
        || typeof(theRow.style) == 'undefined') {
        return false;
    }

    // 2. Gets the current row and exits if the browser can't get it
    if (typeof(document.getElementsByTagName) != 'undefined') {
        theCells = theRow.getElementsByTagName('td');
    }
    else if (typeof(theRow.cells) != 'undefined') {
        theCells = theRow.cells ;
    }
    else {
        return false;
    }

    // 3. Gets the current color...
    var rowCellsCnt  = theCells.length;
    var domDetect    = null;
    var currentColor = null;
    var newColor     = null;
    // 3.1 ... with DOM compatible browsers except Opera that does not return
    //         valid values with "getAttribute"
    if (typeof(window.opera) == 'undefined'
        && typeof(theCells[0].getAttribute) != 'undefined') {
        currentColor = theCells[0].getAttribute('bgcolor');
        domDetect    = true;
    }

 // 3.2 ... with other browsers
    else {
        currentColor = theCells[0].style.backgroundColor;
        domDetect    = false;
    } // end 3
    // 3.3 ... Opera changes colors set via HTML to rgb(r,g,b) format so fix it

    if (currentColor.indexOf("rgb") >= 0)
    {
        var rgbStr = currentColor.slice(currentColor.indexOf('(') + 1,
                                     currentColor.indexOf(')'));
        var rgbValues = rgbStr.split(",");
        currentColor = "#";
        var hexChars = "0123456789ABCDEF";
        for (var i = 0; i < 3; i++)
        {
            var v = rgbValues[i].valueOf();
            currentColor += hexChars.charAt(v/16) + hexChars.charAt(v%16);
        }
    }

    // 4. Defines the new color
    // 4.1 Current color is the default one
    if (currentColor == ''
        || currentColor.toLowerCase() == theDefaultColor.toLowerCase()) {
        if (theAction == 'over' && thePointerColor != '') {
            newColor              = thePointerColor;
        }
        else if (theAction == 'click' && theMarkColor != '') {
            newColor              = theMarkColor;
            marked_row[theRowNum] = true;
            // Garvin: deactivated onclick marking of the checkbox because it's also executed
            // when an action (like edit/delete) on a single item is performed. Then the checkbox
            // would get deactived, even though we need it activated. Maybe there is a way
            // to detect if the row was clicked, and not an item therein...
            // document.getElementById('id_rows_to_delete' + theRowNum).checked = true;
        }
    }
    // 4.1.2 Current color is the pointer one
    else if (currentColor.toLowerCase() == thePointerColor.toLowerCase()
             && (typeof(marked_row[theRowNum]) == 'undefined' || !marked_row[theRowNum])) {
        if (theAction == 'out') {
            newColor              = theDefaultColor;
        }
        else if (theAction == 'click' && theMarkColor != '') {
            newColor              = theMarkColor;
            marked_row[theRowNum] = true;
            // document.getElementById ('id_rows_to_delete' + theRowNum).checked = true;
        }
    }
    // 4.1.3 Current color is the marker one
    else if (currentColor.toLowerCase() == theMarkColor.toLowerCase()) {
        if (theAction == 'click') {
            newColor              = (thePointerColor != '')
                                  ? thePointerColor
                                  : theDefaultColor;
            marked_row[theRowNum] = (typeof(marked_row[theRowNum]) == 'undefined' || !marked_row[theRowNum])
                                  ? true
                                  : null;
            // document.getElementById('id_rows_to_delete' + theRowNum).checked = false;
        }
    } // end 4

    // 5. Sets the new color...
    if (newColor) {
        var c = null;
        // 5.1 ... with DOM compatible browsers except Opera
        if (domDetect) {
            for (c = 0; c < rowCellsCnt; c++) {
                theCells[c].setAttribute('bgcolor', newColor, 0);
            } // end for
        }
        // 5.2 ... with other browsers
        else {
            for (c = 0; c < rowCellsCnt; c++) {
                theCells[c].style.backgroundColor = newColor;
            }
        }
    } // end 5

    return true;
} // end of the 'setPointer()' function

var marked_row_index = 0;

function select_row(row_id)
{
    var cells_count = 8;
    
    for(i = 1; i <= cells_count; i++) {
        var selected_row = document.getElementById('residue_id_' + marked_row_index + '_' + i);
        if (selected_row != null) {
            selected_row.setAttribute('bgcolor', '#FFFFFF', 0);
        }
    }
    
    for(i = 1; i <= cells_count; i++) {
        var selected_row = document.getElementById('residue_id_' + row_id + '_' + i);
        if (selected_row != null) {
            marked_row_index = row_id;
            selected_row.setAttribute('bgcolor', '#FFCC99', 0);
        }
    }
    return false;
}

function create_bookmark(title, url)
{
	if (window.sidebar) { // Mozilla Firefox Bookmark
		window.sidebar.addPanel(title, url, "");
	} else if( window.external ) { // IE Favorite
		window.external.AddFavorite(url, title); }
	else if(window.opera && window.print) { // Opera Hotlist
		return true;
	}
}

function print_page()
{
	window.print();
}

function email(user, domain)
{
    var string = user + '@' + domain;
    return string;
}
//server registration and edit forms 
var Param = new Array();
function GetParam() {
	Param["request_url"] = document.getElementById("request_url").value;
	Param["email"] = document.getElementById("email").value;
	Param["email_key"] = document.getElementById("email_key").value;
	Param["target_name_key"] = document.getElementById("target_name_key").value;
	Param["sequence_key"] = document.getElementById("sequence_key").value;
	Param["other"] = document.getElementById("other").value;
}
function SetUrl() {
GetParam();
	document.getElementById("server_format").innerHTML = Param["request_url"] +
	"?"+ Param["sequence_key"] + "=" + "AFCDELMKDTKTW"
	+ "&" +Param["email_key"] + "=servers@predictioncenter.org"
	+ "&" + Param["target_name_key"] + "=TargetName"
	+ "&" + Param["other"];
}

function escramble(user,domain){
 var a,b,c,d,e,f,g,h,i
 a='<a href=\"mai'
 b=user
 c='\">'
 a+='lto:'
 b+='@'
 e='</a>'
 f=''
 b+=domain
 g='<img src=\"'
 h=''
 i='\" alt="Email us." border="0">'
 if (f) d=f
 else if (h) d=g+h+i
 else d=b
 document.write(a+b+c+d+e)
}

//DATA GRID

function reset_ms(order,field) {
	var msEl= document.getElementById('multi_sort');
	msEl.value = "";
}
function sort_table(order,field) {
    document.getElementById('order').value = order;
    document.getElementById('field').value = field;
	var msEl= document.getElementById('multi_sort');
	if(msEl != null && msEl.checked) {
		msEl.value = msEl.value + "," + field + " " + order;
	}
	//alert(msEl.value);             
	//alert(document.getElementById('field').value);
	document.getElementById('submit').click();
}

function show_results(show_type, el_id) {
    document.getElementById(el_id).value = show_type;            
    document.getElementById('submit').click();
    //document.getElementById('view').value= "results";
}

function show_breif_full_results(show_type, el_id) {
    if(show_type == 'brief') {show_type = 'full'} else {show_type = 'brief'}
    show_results(show_type, el_id);
}

function row_over(oThis) {
	oThis.setAttribute("className", "rw");
	oThis.setAttribute("class", "rw");
}

function row_out(oThis) {
	oThis.setAttribute("className", "");
	oThis.setAttribute("class", ""); 

}