var qstr = "empty";
var newWin;


function openWindow(address)
{ 
	newWin = window.open(address,'_help','personalbar=0, toolbar=0,location=0,directories=0,menuBar=0,status=0,resizable=yes,scrollBars=0, resizable=1, width=800, height = 500,top=0,left=0'); 
    newWin.resizeTo(800, 500);
    newWin.focus();
}

function openWindow2(address)
{ 
	newWin = window.open(address,'_pic','personalbar=0, toolbar=0,location=0,directories=0,menuBar=0,status=0,scrollBars=0, resizable=1, width=587, height = 445,top=0,left=0'); 
    newWin.focus();
}


function openWindowScroll(address)
{ 
	newWin = window.open(address,'_help','personalbar=0, toolbar=0,location=0,directories=0,menuBar=0,status=0,resizable=yes,scrollBars=1, resizable=1, width=800, height = 500,top=0,left=0'); 
    newWin.resizeTo(800, 500);
    newWin.focus();
}

function openWindowMenus(address)
{
	newWin = window.open(address,'_link','personalbar=1, toolbar=1,location=1,directories=1,menuBar=1,status=1,resizable=yes,scrollBars=1, resizable=1, width=800, height = 500,top=0,left=0');
    newWin.resizeTo(800, 500);
    newWin.focus();
}

function MM_swapImgRestore() { //v3.0
  var i,x,a=document.MM_sr; for(i=0;a&&i<a.length&&(x=a[i])&&x.oSrc;i++) x.src=x.oSrc;
}

function MM_preloadImages() { //v3.0
  var d=document; if(d.images){ if(!d.MM_p) d.MM_p=new Array();
    var i,j=d.MM_p.length,a=MM_preloadImages.arguments; for(i=0; i<a.length; i++)
    if (a[i].indexOf("#")!=0){ d.MM_p[j]=new Image; d.MM_p[j++].src=a[i];}}
}

function MM_findObj(n, d) { //v4.0
  var p,i,x;  if(!d) d=document; if((p=n.indexOf("?"))>0&&parent.frames.length) {
    d=parent.frames[n.substring(p+1)].document; n=n.substring(0,p);}
  if(!(x=d[n])&&d.all) x=d.all[n]; for (i=0;!x&&i<d.forms.length;i++) x=d.forms[i][n];
  for(i=0;!x&&d.layers&&i<d.layers.length;i++) x=MM_findObj(n,d.layers[i].document);
  if(!x && document.getElementById) x=document.getElementById(n); return x;
}

function MM_swapImage() { //v3.0
  var i,j=0,x,a=MM_swapImage.arguments; document.MM_sr=new Array; for(i=0;i<(a.length-2);i+=3)
   if ((x=MM_findObj(a[i]))!=null){document.MM_sr[j++]=x; if(!x.oSrc) x.oSrc=x.src; x.src=a[i+2];}
}

function fixQueryTerm (qstr) {
	if (qstr == null) return null;
	
	qstr = qstr.replace(/[\@\&\|\;\>\<\[\]\(\)\{\}]+/g, "");
	qstr = qstr.replace(/\*\*+/g, "*");
	qstr = qstr.replace(/ \*$/g, "");
	qstr = qstr.replace(/ \* /g, "");
	qstr = qstr.replace(/^\* /g, "");
	qstr = qstr.replace(/\s+$/, "");
	qstr = qstr.replace(/^\s+/, "");
	qstr = qstr.replace(/\s+/g, " ");

	return qstr;
}
	

function querySRS(db, qstr) {
	querySRSExtended(db, qstr, null);
}

// extra terms should be a comma delimited list of srs terms, e.g "swall-Keywords:complete proteome, swall-NCBI_TaxID:56636"
function querySRSExtended(db, qstr, extraterms) {

	var defview = "";
	var query = "";
	var bits;
	var i;
	var url ="";
	
	// strip extras away from query string...
	qstr = fixQueryTerm(qstr);
	// do the same to extra terms in case anyone's doing something silly
	if (extraterms != null)
		extraterms = fixQueryTerm(extraterms);

	if(!qstr || qstr == "" || qstr == "*" || qstr.length > 200) {
		void(qstr=prompt("Search for:",""));
	}
  
	if (qstr && qstr != "" && qstr != "*" && qstr.length < 201) {
		if (qstr.indexOf(" ") > 0) {
			bits = qstr.split(" ");
			for (i=0; i<bits.length; i++) {
				if (bits[i].length > 1) bits[i] += '*';
			}
			if (qstr.indexOf("*") < 0) qstr += "*";
			query = escape(qstr) + escape("|") + "("+ escape(bits.join("&")) + ")";
			bits = null;
		} else {
			if (qstr.indexOf("*") < 0 && qstr.length > 1) qstr += "*";
			query = escape(qstr);	
		}
		// database specific bits and bobs...
		switch (db) {
			case 'CluSTr' : {
				top.location.href="http://www.ebi.ac.uk/servlets/clustr/clustr/display/CReport?swall-alltext="+query ;
				return;
			}
			case 'MEDLINE' : {
				defview = "+-vn+3+-page+qResult";
				break;
			}
			case 'INTERPRO' : {   
				defview = "+-view+InterproTable+-page+qResult";
				break;
			}
			case 'PDB' : {
				defview= "+-page+qResult";
				break;
			}
			case 'EMBL' : {		
				db = "libs%3d{embl%20emblcon}";
			}
			default : {
				defview= "+-view+SeqSimpleView+-page+qResult";
				break;
			}
		}
		
		url = "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+["+db+"-AllText:"+query+"]";
		
		if (extraterms != null) {
			bits = extraterms.split(",");
			for (i=0; i<bits.length; i++) {
				if (bits[i].length > 0) url += escape('&') + "[" + escape(bits[i]) + "]";	
			}
		}
		
		url += "+-lv+30"+defview ;
		
		top.location.href=url;
		
	} else {
    	//do nothing
    } 
}

function gethelp(db) {

     if (db=='CluSTr') {
 	  	location.href='http://www3.ebi.ac.uk/~sp/intern/projects2/cluster/clust.html'
	 } else if (db.indexOf('EMBL')>0) {
        location.href='http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+EMBL';
     } else {
        location.href='http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+'+db;
     }
}

function gotoPrintable() {
	window.top.location = "http://www.ebi.ac.uk/cgi-bin/printable?f=" + document.location;
	return false;
}