var currentMatch = null;
var currentMut = null;

// hME-10, us5, us510, us8, us810
var list = new Array("ACGTTGGATG",
                     "AGCGGATAACAATTTCACACAGG",
                     "AGCGGATAAC",
                     "GGCGCACGCCTCCACG",
                     "GGCGCACGCC");

// Concatenate unchecked items for pagination
var unchecked = "";

function jStopMixDefaults() {
  var frm=document.forms[0];
  var stopmix = frm.stopMix.options[frm.stopMix.selectedIndex].value;

  if (stopmix == "hME") {
    frm.byproducts.value = 30;
    frm.resolution.value = 20;
  } else {
    frm.byproducts.value = 0;
    frm.resolution.value = 30;
  }
}

function jGoBrowser(arg1) {
  var frm=document.forms[0];
  var assembly = frm.assemblyb.options[frm.assemblyb.selectedIndex].value;
     
  if ( location.hostname.indexOf( 'cluster' ) != -1 ) {
    var URL = 'https://' + location.hostname;
  } else {
    var URL = 'http://' + location.hostname;
  }
                                                                                                                                                   
  window.location = URL + "/cgi-bin/webseq/applet.cgi?chromParam=" + arg1 + "&assembly=" + assembly;
  //frm.submit();
}

function jGoAdvanced(arg1, arg2, arg3, arg4) {
  var frm=document.forms[1];
  frm.user_choice.value = arg1;
  frm.have_results.value = arg2;

  if (elementExists("last_filename"))
    frm.last_filename.value = arg3;
  frm.jobid.value = arg4;
  frm.advanced_view.value = "true";
  frm.submit();
}

function jSetPrimerTags( arg1, arg2 ) {
  // arg1 = field to set
  // arg2 = field to get index from
  var frm=document.forms[0];
  if (frm.elements[arg2].selectedIndex == 0 || 
      frm.elements[arg2].selectedIndex == 1) {
    frm.elements[arg1].value = "";
  } else {
    frm.elements[arg1].value = list[frm.elements[arg2].selectedIndex - 2];
  }
  return;
}

function jSetHmeTags() {
  var frm=document.forms[0];
  
  jSetPopupElement("primarytag", 1);
  jSetPopupElement("secondarytag", 1);
  return;
}

function jPrextendTaglen() {
  var frm=document.forms[1];

  if (frm.assumetags.checked) {
    frm.sumTagLen.value = 20;  
  }
  return;
}

function jSetTextElement( arg1, arg2 ) {
  // arg1 -> Form element name
  // arg2 -> Value to assign to form element
  var frm=document.forms[0];

  frm.elements[arg1].value = arg2;
  return;
}

function jSetPopupElement( arg1, arg2 ) {
  // arg1 -> Form element name
  // arg2 -> Index to assign to form element
  var frm=document.forms[0];

  frm.elements[arg1].selectedIndex = arg2;
  return;
}

function jOligoPricing() {
  var frm=document.forms[0];
  window.open( "", "snpwindow", "height=450,width=450" );
  frm.target = "snpwindow";
  frm.oligoprice.value="oligoprice";
  frm.submit();
  return;
}   

function jMatchFocus( ) {
  var frm=document.forms[0];
  currentMatch = frm.matchBases.options[frm.matchBases.selectedIndex].value;  
}

function jMutFocus( ) {
  var frm=document.forms[0];
  currentMut = frm.mutations.options[frm.mutations.selectedIndex].value;
}

function jMutCheck( ) {
  var frm=document.forms[0];
  if ( frm.mutations.options[frm.mutations.selectedIndex].value == "0" ) {
    frm.matchBases.selectedIndex = 11;
  } else if ( currentMut == 0 ) { 
    frm.matchBases.selectedIndex = 3;
  }
  frm.mutations.blur();
}

function jMatchCheck() {
  var frm=document.forms[0];
  if ( frm.matchBases.options[frm.matchBases.selectedIndex].value == "All" ) {
    frm.mutations.selectedIndex = 0;
  } else if ( currentMatch == "All" ) {
    frm.mutations.selectedIndex = 1;
  }
  frm.matchBases.blur();
}



function jSetExtendTag() {
  var frm=document.forms[0];
  var list = new Array("ACGTTGGATG",
                       "AGCGGATAACAATTTCACACAGG",
                       "AGCGGATAAC",
                       "GGCGCACGCCTCCACG",
                       "GGCGCACGCC");
  frm.expectedTags.value = list[frm.expectedTags2.selectedIndex];
}

function getNodeFromFolder( arg ) {
  var tree = NTrees['Tree'];
  var urlstr;
  var re;
  for ( var i = 0; i < tree.Nodes.length; i++ ) {
    urlstr = tree.Nodes[i].url;
    re = new RegExp( "folder=" + arg ); 
    if ( urlstr.match( re ) ) {
      return i;
    }
  }
}

function setCheck( name, checked ) {
  // name = checkbox name
  // checked = true or false
  var frm=document.forms[0];
  for (var i = 0; i < frm.elements.length; i++) {
    var f = frm.elements[i];
    if (f.name == name ) {
      frm.elements[name].checked=checked;
    }
  }
}

function jSaveProfile() {
  var frm=document.forms[0];
  frm.act.value = "Save";
  frm.submit();
}


function jOligo( arg1 ) {
  var frm=document.forms[0];
  if (jSelected(frm, 'check')) {
    for (var i = 0; i < frm.elements.length; i++) {
      var f = frm.elements[i];
      if (f.name == 'check' && f.checked==true ) {
        frm.user_choice.value="oligo";
      }
    }
    frm.dir.value = arg1;
    frm.submit();
  } else {
    alert('Nothing was Selected');
    return;
  }
}
function getCookie(c_name)
{
if (document.cookie.length>0)
  {
  c_start=document.cookie.indexOf(c_name + "=");
  if (c_start!=-1)
    { 
    c_start=c_start + c_name.length+1; 
    c_end=document.cookie.indexOf(";",c_start);
    if (c_end==-1) c_end=document.cookie.length;
    return unescape(document.cookie.substring(c_start,c_end));
    } 
  }
return "";
}

function setCookie(c_name,value,expiredays)
{
	var exdate=new Date();
	exdate.setDate(exdate.getDate()+expiredays);
	document.cookie=c_name+ "=" +escape(value)+
	((expiredays==null) ? "" : ";expires="+exdate.toGMTString());
}

function checkCookie()
{
	setCookie('cookiename','epidesignercookietest',5);
	username=getCookie('cookiename');
	var retValue=true;
	if (username!='epidesignercookietest')
	  {
		retValue=false;
	  }
	setCookie('cookiename','epidesignercookietest',-500);
	return retValue;
}

function jChoiceMP(){
autofitIframe('contentFRM');
if(!checkCookie()){
alert('Enable cookies to continue');
return;
}
  var frm = document.forms[1];
 
  if((frm.upload.value == "" || frm.upload.value == undefined)&&(frm.sequence.value == "" || frm.sequence.value==undefined)){
	alert("An input file or a sequence is required");
	return;
	}
if( !(frm.elements['maximize_coverage'].checked) && (frm.elements['primer_num_return'].value=="" || frm.elements['primer_num_return'].value==undefined)){
	alert("Number of output primers is required");
	return;
}	
  frm.user_choice.value = 'startmp';
//if(frm.elements['batch_mode'].checked){
//parent.document.getElementById("vertical").cols="0,100";
//}
  frm.submit();
}

function jChoiceExtend( arg ) {
  var frm = document.forms[1];
  frm.user_choice.value = arg;
  if (elementExists("primarytagtext")) {
    if (/[^agct]/i.test(frm.primarytagtext.value)) {
      alert("Custom Primary Tags must contain combinations of 'AGCT' only");
      return;
    } else if (/[^agct]/i.test(frm.secondarytagtext.value)) {
      alert("Custom Secondary Tags must contain combinations of 'AGCT' only");
      return;
    }
  }
  if (elementExists("upload")) {
    //if (/[\s\t!@#$%^&*()]/i.test(frm.upload.value)) {
    //  alert("Invalid File name:  Please avoid spaces and the "+
    //        "following characters\n in your filename or path '!@#$%^*()'\"{}[]<>"); 
    //  return;
    //} 
  }
  if ( frm.upload.value == "" )
    alert( "An Input File is required" );
  else
    frm.submit();
}

function jChoicePrextend( arg ) {
  var frm = document.forms[1];
  frm.user_choice.value = arg;
  if ( parseInt( frm.minAmpLen.value ) < 50 )
    alert( "The Minimum Amplicon Length with tags must be greater than 50bp" );
  else if ( parseInt( frm.minAmpLen.value ) > parseInt( frm.optAmpLen.value ) )
    alert( "The Optimal Amplicon Length with tags must be greater than the Minimum Amplicon Length" );
  else if ( parseInt( frm.maxAmpLen.value ) < parseInt( frm.optAmpLen.value ) )
    alert( "The Maximum Amplicon Length must be greater than the Optimal Amplicon Length" );
  else if ( parseInt( frm.maxAmpLen.value ) > 500 ) 
    alert( "The Maximum Amplicon Length must be less than 500" );
  else if ( parseInt( frm.maxAmps.value ) > 1000 || parseInt( frm.maxAmps.value ) < 0 ) 
    alert( "Maximum Amplicons must be between 0 and 1000" );
  else if ( parseInt( frm.sumTagLen.value ) > 100 || parseInt( frm.sumTagLen.value ) < 0 )
    alert( "Sum Tag Length must be a value between 1 and 100" );
  else if ( frm.upload.value == "" )
    alert( "An Input File is required" );
  else {
    //if (/[\s\t!@#$%^&*()]/i.test(frm.upload.value)) {
    //  alert("Invalid File name:  Please avoid spaces and the "+
    //        "following characters\n in your filename or path '!@#$%^*()'\"{}[]<>");
    //  return;
    //} else {
      frm.submit();
    //}
  }
}

function jChoiceDesign( arg ) {
  var frm = document.forms[1];
  var error = false;
  frm.user_choice.value = arg;
  if ( parseInt( frm.ampliconmin.value ) < 50 ) {
    alert( "The Minimum Amplicon Length with tags must be greater than 50bp" );
    return;
  }
  if ( parseInt( frm.ampliconmin.value ) > parseInt( frm.ampliconopt.value ) ) {
    alert( "The Optimal Amplicon Length with tags must be greater than the Minimum Amplicon Length" );
    return;
  }
  if ( parseInt( frm.ampliconmax.value ) < parseInt( frm.ampliconopt.value ) ) {
    alert( "The Maximum Amplicon Length must be greater than the Optimal Amplicon Length" );
    return;
  }
  if ( parseInt( frm.ampliconmax.value ) > 1000 ) {
    alert( "The Maximum Amplicon Length must be less than 500" ); 
    return;
  }
  if ( parseInt( frm.multiplexmin.value ) > parseInt( frm.multiplexmax.value ) ) {
    alert( "The Maximum Multiplex value must be greater than the Minimum value" );
    return;
  }
  if ( parseInt( frm.minEPlen.value ) > parseInt( frm.maxEPlen.value ) ) {
    alert( "The Maximum Primer length value must be greater than the Minimum value" );
    return;
  }
  if ( parseInt( frm.minEPlen.value ) < 15  ) {
    alert( "The Minimum Primer length value must be greater than 14" );
    return;
  }
  if ( parseInt( frm.maxEPlen.value ) > 40  ) {
    alert( "The Maximum Primer length value must be smaller than 41" );
    return;
  }	 
  if ( parseInt( frm.minEPtm.value ) > parseInt( frm.maxEPtm.value ) ) {
    alert( "The Maximum Primer Binding Tm must be greater than the Minimum value" );
    return;
  }
  if ( parseInt( frm.minEPtm.value ) < 10 ) {
    alert( "The Minimum Primer Binding Tm must be greater than 9" );
    return;
  }	
  if ( parseInt( frm.maxEPtm.value ) > 209 ) {
    alert( "The Maximum Primer Binding Tm must be smaller than 210" );
    return;
  } 	
  if ( parseInt( frm.masslimit.value ) > 15000 || parseInt( frm.masslimit.value) < 5400) {
    alert( "The Upper Mass Limit value must be greater than 5,400 and smaller than 15,000 " );
    return;
  }

  if ( elementExists( "upload" ) ) { 
    if ( frm.upload.value == "" ) {
      alert( "An Input File is required" );
      return;
    }
    //if (/[\s\t!@#$%^&*()]/i.test(frm.upload.value)) {
    //  alert("Invalid File name:  Please avoid spaces and the "+
    //        "following characters\n in your filename or path '!@#$%^*()'\"{}[]<>");
    //  return;
    //} 
  }
  if (elementExists("primarytagtext")) {
    if (/[^agct]/i.test(frm.primarytagtext.value)) {
      alert("Custom Primary Tags must only contain combinations of 'AGCT' only");     
      return;
    }
  }
  if (elementExists("secondarytagtext")) {
    if (/[^agct]/i.test(frm.secondarytagtext.value)) {
      alert("Custom Secondary Tags must only contain combinations of 'AGCT' only");
      return;
    }
  }
  frm.submit();
}


function jChoiceDesignQGE( arg ) {
  var frm = document.forms[1];
  var error = false;
  frm.user_choice.value = arg;
  if ( parseInt( frm.ampliconmin.value ) < 50 ) {
    alert( "The Minimum Amplicon Length with tags must be greater than 50bp" );
    return;
  }
  if ( parseInt( frm.ampliconmin.value ) > parseInt( frm.ampliconopt.value ) ) {
    alert( "The Optimal Amplicon Length with tags must be greater than the Minimum Amplicon Length" );
    return;
  }
  if ( parseInt( frm.ampliconmax.value ) < parseInt( frm.ampliconopt.value ) ) {
    alert( "The Maximum Amplicon Length must be greater than the Optimal Amplicon Length" );
    return;
  }
  if ( parseInt( frm.ampliconmax.value ) > 1000 ) {
    alert( "The Maximum Amplicon Length must be less than 500" );
    return;
  }
  if ( parseInt( frm.multiplexmin.value ) > parseInt( frm.multiplexmax.value ) ) {
    alert( "The Maximum Multiplex value must be greater than the Minimum value" );
    return;
  }
  if ( parseInt( frm.poverlapmin.value ) > parseInt( frm.poverlapmax.value ) ) {
    alert( "The Maximum Primer 3' Overlap value must be greater than the Minimum value" );
    return;
  }
  if ( parseInt( frm.minEPlen.value ) > parseInt( frm.maxEPlen.value ) ) {
    alert( "The Maximum Primer length value must be greater than the Minimum value" );
    return;
  }
  if ( parseInt( frm.minEPlen.value ) < 15  ) {
    alert( "The Minimum Primer length value must be greater than 14" );
    return;
  }
  if ( parseInt( frm.maxEPlen.value ) > 40  ) {
    alert( "The Maximum Primer length value must be smaller than 41" );
    return;
  }
  if ( parseInt( frm.minEPtm.value ) > parseInt( frm.maxEPtm.value ) ) {
    alert( "The Maximum Primer Binding Tm must be greater than the Minimum value" );
    return;
  }
  if ( parseInt( frm.minEPtm.value ) < 10 ) {
    alert( "The Minimum Primer Binding Tm must be greater than 9" );
    return;
  }
  if ( parseInt( frm.maxEPtm.value ) > 209 ) {
    alert( "The Maximum Primer Binding Tm must be smaller than 210" );
    return;
  }
  if ( parseInt( frm.resolution.value ) > 1000 || parseInt( frm.resolution.value) < 10) {
    alert( "The Analyte Peak Resolution value must be greater than 9 and smaller than 1,001 " );
    return;
  }
  if ( parseInt( frm.masslimit.value ) > 15000 || parseInt( frm.masslimit.value) < 5400) {
    alert( "The Upper Mass Limit value must be greater than 5,400 and smaller than 15,000 " );
    return;
  }
  if ( elementExists( "upload" ) ) {
    if ( frm.upload.value == "" ) {
      alert( "An Input File is required" );
      return;
    }
    //if (/[\s\t!@#$%^&*()]/i.test(frm.upload.value)) {
    //  alert("Invalid File name:  Please avoid spaces and the "+
    //        "following characters\n in your filename or path '!@#$%^*()'\"{}[]<>");
    //  return;
    //}
  }
  if (elementExists("primarytagtext")) {
    if (/[^agct]/i.test(frm.primarytagtext.value)) {
      alert("Custom Primary Tags must only contain combinations of 'AGCT' only");
      return;
    }
  }
  if (elementExists("secondarytagtext")) {
    if (/[^agct]/i.test(frm.secondarytagtext.value)) {
      alert("Custom Secondary Tags must only contain combinations of 'AGCT' only");
      return;
    }
  }
  frm.submit();
}


function jChoiceProxsnp( arg ) {
  var frm = document.forms[1];
  frm.user_choice.value = arg;
  if ( parseInt( frm.flanking_seq.value ) < 25 || parseInt( frm.flanking_seq.value ) > 500 )
    alert( "The SNP Flanking Sequence value must be between 25 and 500" );
  else if ( parseInt( frm.minAlignLen.value ) < 50 || parseInt( frm.minAlignLen.value ) > 100 )
    alert( "The Minimum Align Length must be between 50 and 100" );
  else if ( parseInt( frm.minAlignHomol.value ) < 50 || parseInt( frm.minAlignHomol.value ) > 100 )
    alert( "The Minimum Align Homology must be between 50 and 100" );
  else if ( parseInt( frm.matchHomol.value ) < 50 || parseInt( frm.matchHomol.value ) > 100 )
    alert( "The Total Matching Homology must be between 50 and 100" );
  else if ( elementExists( "upload" ) ) { 
  if ( frm.upload.value == "" )
    alert( "An Input File is required" );
  }
  else {
    //if (/[\s\t!@#$%^&*()]/i.test(frm.upload.value)) {
    //  alert("Invalid File name:  Please avoid spaces and the "+
    //        "following characters\n in your filename or path '!@#$%^*()'\"{}[]<>");
    //  return;
    //} else {
      frm.submit();
    //}
  }
}

function jChoiceAuto( arg , radioobj) {
  var frm = document.forms[1];
  frm.user_choice.value = arg;
  if ( parseInt( frm.flanking_seq.value ) < 25 || parseInt( frm.flanking_seq.value ) > 500 )
    alert( "The SNP Flanking Sequence value must be between 25 and 500" );
  else if ( parseInt( frm.minAlignLen.value ) < 50 || parseInt( frm.minAlignLen.value ) > 100 )
    alert( "The Minimum Align Length must be between 50 and 100" );
  else if ( parseInt( frm.minAlignHomol.value ) < 50 || parseInt( frm.minAlignHomol.value ) > 100 )
    alert( "The Minimum Align Homology must be between 50 and 100" );
  else if ( parseInt( frm.matchHomol.value ) < 50 || parseInt( frm.matchHomol.value ) > 100 )
    alert( "The Total Matching Homology must be between 50 and 100" );
  else if ( frm.upload.value == "" )
    alert( "An Input File is required" );
  else if(!radioobj[1].checked && !radioobj[0].checked)
    alert( "Please select the input data type" );
  else if(radioobj[1].checked && (frm.species.value == "" || frm.species.value == undefined))
    alert( "The species name is required" );
  else {
    //if (/[\s\t!@#$%^&*()]/i.test(frm.upload.value)) {
    //  alert("Invalid File name:  Please avoid spaces and the "+
    //        "following characters\n in your filename or path '!@#$%^*()'\"{}[]<>");
    //  return;
    //} else {
      frm.submit();
    //}
  }
}

function jChoiceABS( arg ) {
  var frm = document.forms[1];
  frm.user_choice.value = arg;
  if ( frm.upload.value == "" ){
    alert( "An Input File is required" );
  }
  else {
      frm.submit();
  }
}

function jChoiceNew( usrname,orgid,custid, arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8 ) {
  var frm = document.weplexform;
  frm.user_choice.value = arg1;

  	frm.highlight.value = arg2;
  	frm.application.value = arg3;
  	frm.jobid.value = arg4;
  	frm.title.value = arg5;
  	frm.have_results.value = arg6;
  	frm.advanced_view.value = arg7;
  	frm.last_filename.value = arg8;
  if ( arg2 != ''){
  }
  if ( arg3 != ''){
  }
  if ( arg4 != ''){
  }
  if ( arg5 != ''){
  }
  if ( arg6 != ''){
  }
  if ( arg7 != ''){
  }
  if ( arg8 != ''){
  }

  frm.usrname.value = usrname;
  frm.orgid.value = orgid;
  frm.custid.value = custid;
  frm.submit();
}

function jCheckBlast( arg ) {
  var frm = document.forms[0];
  var input = frm.sequence.value;
  var file = frm.upload.value;

  if ( elementExists( "user_choice" ) ) {
    frm.user_choice.value = arg;
  }

  if ( frm.upload.value == "" &&
       frm.sequence.value == "" ) {
    alert("No input: Please enter an upload file or a sequence");
  } else {
    if ( frm.upload.value == "" ) {
      frm.submit();
    } else {
      frm.sequence.value = "";
      frm.submit();
    }
  }
}

function jChoice(  arg ) {
  var frm = document.forms[1];
  frm.user_choice.value = arg;
  frm.submit();
}

function jGeneSort( arg ) {
  var frm = document.forms[0];
  frm.user_choice.value = arg;
  frm.popup.value=frm.sort.options[frm.sort.selectedIndex].value;
  frm.submit();
} 

function jChoiceCheck( arg ) {
  var frm=document.forms[0];
  if (jSelected(frm, 'check')) {
    if ( elementExists( "oligoprice" ) ) {
      frm.oligoprice.value="";
    }
    frm.target = "_top";

    for (var i = 0; i < frm.elements.length; i++) {
      var f = frm.elements[i];
      if (f.name == 'check' && f.checked==true ) {
        frm.user_choice.value = arg;
      }
    }
    frm.submit();
  } else {
    alert('Nothing was Selected!\nPlease reselect oligos to order');
    return;
  }
}

function jChoiceQGE( arg ) {
  var frm = document.forms[0];
  frm.user_choice.value = arg;
  if ( frm.upload.value == "" )
    alert( "An input file is required" );
  else {
      frm.submit();
  }
}

function jPurchase() {
  var frm = document.forms[0];
  if ( elementExists( "getMatch" ) ) {
      frm.getMatch.value = "";
  }

  frm.purchased.value = "purchased";
  frm.submit();
}

function elementExists( arg ) {
  var frm = document.forms[1];
  for (var i = 0; i < frm.elements.length; i++) {
    if (frm.elements[i].name == arg) {
      return true;
    }
  }
  return false;
}

function jRedirectForm() {
  var frm = document.searchForm;
  if ( location.hostname.indexOf( 'cluster' ) != -1 ) {
    var URL = 'https://' + location.hostname;
  } else {
    var URL = 'http://' + location.hostname;
  }

  for (var i = 0; i < frm.elements.length; i++) {
    var e = frm.elements[i];
    if (e.checked) {
      frm.action = URL + '/cgi-bin/webseq/' + e.value + '.cgi';
    }
  }
  frm.submit();
  return;
}

function jCheckAll() {
  var frm=document.table;
  for (var i = 0; i < frm.elements.length; i++) {
    var e = frm.elements[i];
    if (e.name == "check" || e.name == "primer") {
      if (!frm.checkall.checked) {
        if (e.checked == true) {
          unchecked += e.value + ":";
        } 
      } else {
        unchecked = "";
      }
      e.checked = frm.checkall.checked;
    }
  }
}

function jCheckAllGene() {
  var frm=document.forms[0];
  for (var i = 0; i < frm.elements.length; i++) {
    var e = frm.elements[i];
    if (e.name != "checkGene") {
      e.checked = frm.checkGene.checked;
    }
  }
}

function jDelete() {
  //return;
  var frm=document.table;
  if (jSelected(frm, 'check')) {
    if ( confirm("Delete selected items?") ) {
      for (var i = 0; i < frm.elements.length; i++) {
        var f = frm.elements[i];
        if (f.name == 'check' && f.checked==true ) {
          frm.user_choice.value="delete";
        }
      }
      frm.submit();
    }
    //return;
  } else {
    alert('Nothing was Selected');
    return;
  }
}

function jDeleteArgs( args ) {
  var frm=document.forms[0];
  if (jSelected(frm, 'check')) {
    if ( confirm("Delete selected items?") ) {
      for (var i = 0; i < frm.elements.length; i++) {
        var f = frm.elements[i];
        if (f.name == 'check' && f.checked==true ) {
          frm.user_choice.value="delete";
        }
      }
      frm.submit();
    }
    return;
  } else {
    alert('Nothing was Selected');
    return;
  }
}

function jGlobal( arg ) {
  var frm=document.forms[1];
  frm.chromParam.value = arg;
  frm.submit();
  return;
} 

function jClipAdd(args) {
  var frm=document.forms[0];
  if (jSelected(frm, 'check')) {
    if ( elementExists( "getMatch" )) {
      frm.getMatch.value = "";
    }
    window.open( "", "snpwindow", "height=290,width=550" );
    frm.target = "snpwindow";
    for (var i = 0; i < frm.elements.length; i++) {
      var f = frm.elements[i];
      if (f.name == 'check' && f.checked==true ) {
        frm.clip.value="clip_add";
      }
    }
    frm.submit();
    return;
  } else {
    alert('Nothing was Selected');
    return;
  }
}

function jBlast(args) {
  var frm=document.forms[0];
  if (jSelected(frm, 'check')) {
    if ( confirm("Blast selected SNPs?") ) {
      for (var i = 0; i < frm.elements.length; i++) {
        var f = frm.elements[i];
        if (f.name == 'check' && f.checked==true ) {
          frm.blast.value="blast";
        }
      }
      frm.submit();
    }
    return;
  } else {
    alert('Nothing was Selected');
    return;
  }
}

function jProcess( arg1, arg2, arg3 ) {
  // arg1 -> Confirm dialog box text
  // arg2 -> Value to assign to form element
  // arg3 -> Form element name
  var frm=document.forms[0];

  if ( jSelected(frm, 'check') ) {
    if ( confirm( arg1 ) ) {
      frm.elements[arg3].value = arg2;
      frm.submit();
    }
    return;
  } else {
    alert('Nothing was Selected');
    return;
  }
}

function jClipDeleteAll() {
  var frm=document.forms[0];
    if ( confirm("Clear Entire SNPortfolio?")) {
      frm.deleteAll.value = "yes";
      frm.act.value="delete";
      frm.submit();
    }
    return;
}

function jSelected( frm,chk_box_name ) {
  var selected=false;
  for (var i=0;i<frm.elements.length;i++) {
    var f = frm.elements[i];
    if (f.name == chk_box_name && f.checked==true ) {
      selected = true;
      break;
    }
  }
  return selected;
}

function GetFormElementByName( frm, e_name, e_type ) {
  var e_ptr=null;
  for (var i=0;i<frm.elements.length;i++) {
    var e = frm.elements[i];
    if (e.name == e_name && e.type==e_type) {
      e_ptr = e;
      break;
    }
  }
  return e_ptr;
}

function GetActPtr( frm ) {
  var tmp = GetFormElementByName( frm, 'act', 'hidden');
  if ( tmp == null ) { tmp = GetFormElementByName( frm, 'ImgAct', 'hidden'); }
  if ( tmp != null ) { tmp.name = "act"; }
  return tmp;
}

function jLocus() {
  var frm=document.forms[0];
  frm.elements[3].value = "";
  frm.locus.selectedIndex = -1;
  frm.pop.value=frm.dbase.options[frm.dbase.selectedIndex].value;
  frm.submit();
  return;
}


function jAssembly() {
  var frm=document.forms[0];
  frm.genome_assembly.value=frm.assembly.options[frm.assembly.selectedIndex].value;
  frm.submit();
  return;
}


function jProfile( act, jobid ) {
  var frm=document.forms[0];
  frm.act.value = act;
  frm.jobid.value = jobid; 
  frm.prof.value = frm.profile.options[frm.profile.selectedIndex].value;
  frm.submit();
  return;
}

function jLocusSelect() {
  var frm=document.forms[0];

  frm.elements[3].value = "";
  frm.locus.selectedIndex = -1;
  frm.let.value=frm.letter.options[frm.letter.selectedIndex].value;
  frm.submit();
  return;
}

function jLocusSelectAdv() {
  var frm=document.locus;
  if ( location.hostname.indexOf( 'cluster' ) != -1 ) {
    var URL = 'https://' + location.hostname;
  } else {
    var URL = 'http://' + location.hostname;
  }


  frm.elements[4].value = "";
  frm.locus.selectedIndex = -1;
  frm.let.value=frm.letter.options[frm.letter.selectedIndex].value;
  frm.action = URL + "/cgi-bin/webseq/index.cgi";
  frm.submit();
  return;
} 

function jAdvanced() {
  var frm=document.locus;
  if ( location.hostname.indexOf( 'cluster' ) != -1 ) {
    var URL = 'https://' + location.hostname;
  } else {
    var URL = 'http://' + location.hostname;
  }

  frm.action = URL + "/cgi-bin/webseq/advanced.cgi";
  frm.submit();
  return;
}

function jClipboard() {
  var frm=document.forms[0];
  frm.pop.value=frm.dbase.options[frm.dbase.selectedIndex].value;
  frm.submit();
  return;
}

function jSubmit() {
  document.forms[0].submit();
}

function jTableView() {
  var frm=document.forms[0];
  frm.user_choice.value = "general";
  frm.submit();
  return;
} 

function jHistogram() {
  var frm=document.forms[0];
  if ( elementExists( "clip" ) ) {
    frm.clip.value = "";
    frm.target = "";
  } 
  frm.user_choice.value = "global";
  frm.submit();
  return;
}

function jSubmitAct( arg ) {
  var frm=document.forms[0];
  frm.act.value = arg;
  frm.submit();
}

function jSubmitActDesigner( arg1, arg2 ) {
  var frm=document.forms[0];
  var s = "You are about to commence a SpectroPLEX Run\n" +
          "Your SNPCredits will be debited " + arg1 + " snpcredits \n" +
          "Do you wish to continue?";
  if ( confirm( s ) ) {
    frm.user_choice.value = arg2;
    frm.submit();
  }
}


function jSubmit2(arg) {
  var frm=document.forms[0];
  if ( elementExists( "clip" ) ) {
    frm.clip.value = "";
    frm.target = "";
  }
  if ( elementExists( "getMatch" ) ) {
    frm.getMatch.value = "";
  }

  if ( elementExists( "user_choice" ) ) {
    frm.user_choice.value = "general";
  }
 
  frm.popup.value=frm.sort.options[frm.sort.selectedIndex].value;
  frm.temp.value=arg;
  frm.format.value="";
  frm.submit();
  return;
}

function jSubmitMysnps( arg1, arg2, arg3 ) {
  var frm=document.forms[0];
  if ( elementExists( "clip" ) ) {
    frm.clip.value = "";
    frm.target = "";
  }
  if ( elementExists( "getMatch" ) ) {
    frm.getMatch.value = "";
  }

  frm.popup.value=frm.sort.options[frm.sort.selectedIndex].value;
  frm.temp.value=arg1;
  frm.tsort.value=arg2;
  frm.dir.value=arg3;
  frm.format.value="";
  frm.submit();
  return;
}

function jSort( sort, view, direction ) {
  var frm=document.table;
  if ( elementExists( "clip" ) ) {
    frm.clip.value = "";
    frm.target = "";
  }
  if ( elementExists( "getMatch" ) ) {
    frm.getMatch.value = "";
  }

  frm.popup.value = sort;
  frm.temp.value = view;
  frm.user_choice.value = view;
  //frm.tsort.value=arg3;
  frm.dir.value = direction;
  frm.format.value = "";
  frm.submit();
  return;
}   

function jSubmitResults(arg) {
  var frm=document.forms[0];
  frm.popup.value=frm.sort.options[frm.sort.selectedIndex].value;
  frm.minHomology.value=frm.minHomol.value;
  frm.minAlign.value=frm.minAl.value;
  frm.maxDiffs.value=frm.mxDiff.value;
  frm.maxGaps.value=frm.mxGap.value;
  frm.temp.value=arg;
  frm.submit();
  return;
}

function jSub(arg, dbase) {
  var frm=document.forms[0];
  frm.minHomology.value=frm.minHomol.options[frm.minHomol.selectedIndex].value;
  frm.minAlign.value=frm.minAl.options[frm.minAl.selectedIndex].value;
  frm.minAlign.value=frm.minAl.options[frm.minAl.selectedIndex].value;
  frm.maxDiffs.value=frm.mxDiff.options[frm.mxDiff.selectedIndex].value;
  frm.maxGaps.value=frm.mxGap.options[frm.mxGap.selectedIndex].value;
  //frm.res_format.value=frm.rs_format.options[frm.rs_format.selectedIndex].value;
  //frm.pathJset.value = frm.path.options[frm.path.selectedIndex].value;
  //if (frm.unique.checked) {
  //  frm.uniqueJset.value = "ON";
  //}
  frm.act.value="search";
  frm.user_choice.value = "search";
  frm.actid.value=arg;
  frm.dbase.value=dbase;
  frm.submit();
  return;
}

function jSubmitShow( sort ) {
  var frm=document.forms[0];
  frm.user_choice.value = "";
  frm.pop1.value = sort;
  frm.pop2.value = frm.show.options[frm.show.selectedIndex].value;
  frm.submit();
  return;
}

function jShow( sort ) {
  var frm=document.forms[0];
  //frm.db.value=frm.dbase.options[frm.dbase.selectedIndex].value;
  frm.popup.value = sort;
  frm.popshow.value=frm.show.options[frm.show.selectedIndex].value;
  frm.submit();
  return;
}

function jView( arg ) {
  var frm=document.forms[0];
  frm.format.value = frm.formatSelect.options[frm.formatSelect.selectedIndex].value;
  frm.user_choice.value=arg;
  for (var i = 0; i < frm.elements.length; i++) {
    if (frm.elements[i].name== "clip") {
      frm.clip.value = "";
    }
  }

  //frm.clip.value = "";
  frm.target = "";
  if ( frm.format.value == "importer" ) {
    if ( arg == "schr" || arg == "sloc" || arg == "seq" || arg == "sasy" || arg == "sdet" ) {
      frm.format.value = "";
      if ( frm.getMatch ) {
        frm.getMatch.value = "";
      }
    }
  } else {
    if ( frm.getMatch ) {
      frm.getMatch.value = "";
    }
  }

  frm.create_session.value = "no";
  frm.unchecked.value = unchecked;

  frm.submit();
  return;
}

function jShowSnp( arg ) {
  var frm=document.forms[0];
  if (jSelected( frm, 'check' ) ) {
    frm.popup.value = '';
    frm.checkall.value = 'OFF';
    //frm.user_choice.value = 'showsnp';
    frm.user_choice.value = arg;
    frm.pathJset.value = frm.path.value; 
    //frm.uniqueJset.value = frm.unique.value;
    frm.submit();
    return;
  } else {
    alert( "Please select Genes" );
    return;
  }
}

function jDesigner() {
  var frm=document.forms[0];
  if (jSelected( frm, 'check' ) ) {
    frm.popup.value = '';
    frm.checkall.value = 'OFF';
    frm.user_choice.value = 'showsnp';
    frm.pathJset.value = frm.path.value; 
    frm.uniqueJset.value = frm.unique.value;
    frm.submit();
    return;
  } else {
    alert( "Please select SNPs to run" );
    return;
  } 
}

function jPageBackup( offset, choice, sort, direction ) {
  var frm=document.forms[0];
  for (var i = 0; i < frm.elements.length; i++) {
    var f = frm.elements[i];
    if ( f.name == 'checkall' ) {
      f.checked = false;
    }
    if ( f.name == 'check' ) {
      f.checked = false;
    }
  }
                                                                                                                                 
  if ( elementExists( "getMatch" ) ) {
    frm.getMatch.value = "";
  }
  if ( elementExists( "user_choice" ) ) {
    frm.user_choice.value = choice;
  }
  if ( elementExists( "purchased" ) ) {
    frm.purchased.value = "purchased";
  }
  if ( elementExists( "clip" ) ) {
    frm.clip.value="";
  }
                                                                                                                                 
  frm.target = "";
  frm.dir.value = direction;
  frm.popup.value = sort;
  frm.off.value = offset;
  frm.temp.value = choice;
  frm.submit();
  return;
}

function jClearChecks() {
  var frm=document.forms[0];
  for (var i = 0; i < frm.elements.length; i++) {
    var f = frm.elements[i];
    if ( f.name == 'checkall' ) {
      f.checked = false;
    }
    if ( f.name == 'check' ) {
      f.checked = false;
    }
  }
}

function jSetCheckOn(name, value) {
  var frm=document.forms[0];
  for (var i = 0; i < frm.elements.length; i++) {
    var f = frm.elements[i];
    if ( f.name == name && f.value == value ) {
      f.checked = true;
    }
  }
}

function jCheckUnchecked(name, value) {
  var frm=document.forms[0];
  for (var i = 0; i < frm.elements.length; i++) {
    var f = frm.elements[i];
    if ( f.name == name && f.value == value ) {
      if (f.checked == false) {
        unchecked += value + ":";
      }
    }
  }
}

function jPage( offset, choice, sort, direction ) {
  //jClearChecks();
  var frm=document.forms[0];
  if ( elementExists( "getMatch" ) ) {
    frm.getMatch.value = "";
  }
  if ( elementExists( "user_choice" ) ) {
    frm.user_choice.value = choice;
  }
  if ( elementExists( "purchased" ) ) {
    frm.purchased.value = "purchased";
  }
  if ( elementExists( "clip" ) ) {
    frm.clip.value="";
  }

  frm.target = "";
  frm.dir.value = direction;
  frm.popup.value = sort;
  frm.off.value = offset;
  frm.temp.value = choice; 
  frm.create_session.value = "no";
  frm.unchecked.value = unchecked;
  frm.submit();
  return;
}

function setLow() {
  var frm=document.forms[0];
  frm.loValue.value = LOW[frm.elements[4].selectedIndex];
}

function setHigh() {
  var frm=document.forms[0];
  frm.hiValue.value = HIGH[frm.elements[6].selectedIndex];
} 

function jMatch() {
  var frm=document.forms[0];
  frm.getMatch.value = "getMatch";
  frm.submit(); 
  return;
}

function setAnno() {
  var frm=document.forms[0];
  frm.pathJset.value = frm.path.options[frm.path.selectedIndex].value;
  frm.submit();
  return;
}

function jUnique() {
  var frm=document.forms[0];
  if ( elementExists( "clip" ) ) {
    frm.clip.value = "";
    frm.target = "";
  }
  if ( elementExists( "getMatch" ) ) {
    frm.getMatch.value = "";
  }
  if (frm.unique.checked) {
    frm.uniqueJset.value = "ON";
  } else {
    frm.uniqueJset.value = "";
  }

  if ( elementExists( "user_choice" ) ) {
    //frm.user_choice.value = "";
  }

  frm.submit();
  return;
}

function jAnnotate () {
  var frm=document.forms[0];
  frm.pathJset.value=frm.path.options[frm.path.selectedIndex].value;
  frm.submit();
  return;
}


function qgeTerms() {
  var frm=document.forms[0];
  for (var i=0; i<4; i++) {
    if (frm.user_choice[i].checked == true)  {
      var type = frm.user_choice[i].value;
    }
  }
  window.open('/webseq/qge_terms.html' + '?user_choice=' + type,'terms','resizable=yes,scrollbars=yes,width=700,height=600');
  return;
}

function jNonHuman(radioobj,url){
if(radioobj[1].checked){
document.getElementById('nonhuman_div').style.display='block';
document.getElementById('nonhuman_div2').style.display='block';
//window.open(url);
}
else{
document.getElementById('nonhuman_div').style.display='none';
document.getElementById('nonhuman_div2').style.display='none';
}
}

function jOrderABS(cat1,id1,price){
  var frm=document.forms[1];
  frm.item_category.value=cat1;
  frm.item_id.value=id1;
  frm.price.value=price;
  frm.submit();
}

function jCoverage(max_coverage){
if(max_coverage.checked){
document.MainBlastForm.primer_num_return.disabled=true;
//document.getElementById('max_coverage_div1').style.display='none';
//document.getElementById('max_coverage_div2').style.display='none';
}
else{
document.MainBlastForm.primer_num_return.disabled=false;
//document.getElementById('max_coverage_div1').style.display='block';
//document.getElementById('max_coverage_div2').style.display='block';
}
}

function jDescTier(divid,linkid,dsite){
if(divid == "price_div"){

if (document.getElementById(divid).style.display == 'none'){
document.getElementById(linkid).innerHTML='Hide ';
document.getElementById(divid).style.display='block';
}
else{
document.getElementById(divid).style.display='none';
document.getElementById(linkid).innerHTML='View ';
}
return;
}
if (document.getElementById(divid).style.display == 'none'){
document.getElementById(linkid).innerHTML='<img src='+dsite+'/snpimages/minusnode.gif width=12 height=12 border=0>';
document.getElementById(divid).style.display='block';
}
else{
document.getElementById(divid).style.display='none';
this.innerHTML='expand';
document.getElementById(linkid).innerHTML='<img src='+dsite+'/snpimages/plusnode.gif width=12 height=12 border=0>';
}
}

function jDownloadPrimers(arg){
var frm=document.table;
frm.user_choice.value=arg;
if(arg=='download'){
  if (jSelected(frm, 'check')) {
  }
  else{
    alert('Nothing was Selected');
    return;
  }
}
frm.submit();
}

function jDeletePrimers(){
  var frm=document.table;
  if (jSelected(frm, 'check')) {
    if ( confirm("Delete selected items?") ) {
      for (var i = 0; i < frm.elements.length; i++) {
        var f = frm.elements[i];
        if (f.name == 'check' && f.checked==true ) {
          frm.user_choice.value="deletep";
        }
      }
      frm.submit();
    }
    //return;
  } else {
    alert('Nothing was Selected');
    return;
  }
}

function jResizeFrame(arg1,arg2){
	parent.document.getElementById("vertical").rows=arg1;
	parent.frames.vertical.rows=arg1;
		//alert(parent.document.getElementByName('ResultsWindow').src+','+arg2);
	if(arg2 == 'no'){
		parent.document.getElementByName('ResultsWindow').src='/blank.html';
	}
	//parent.document.getElementById("LeftWindow").frameborder=1;
}

function jExportPrimers(arg){
  var frm=document.table;
	//alert(frm.elements['export_type']);
  if (jSelected(frm, 'primer')) {
if(arg == "save"){
  frm.elements['export_type'].value='save';
}
else{
  frm.elements['export_type'].value=frm.elements['export_format'].value;
}
 frm.submit();
  } else {
    alert('Nothing was Selected');
    return;
  }
}
function jToggleSeq(divid,linkid){

if (document.getElementById(divid).style.display == 'none'){
document.getElementById(linkid).innerHTML='Hide ';
document.getElementById(divid).style.display='block';
}
else{
document.getElementById(linkid).innerHTML='View ';
document.getElementById(divid).style.display='none';
}
}

function jSelectPrimer(arg){
  var frm=document.forms[0];
  for (var i = 0; i < frm.elements.length; i++) {
    var f = frm.elements[i];
    if (f.name == 'primer' && f.value == arg) {
      f.checked='true';
    }
  }
}

function jEmailOrder(){
  var frm=document.table;
	frm.user_choice.value='order';
	frm.submit();
  /*if (jSelected(frm, 'check')) {
  } else {
    alert('Nothing was Selected');
    return;
  }*/
}
function jSubmitOrder(){
  var frm=document.frm;

  if(isValueNull('first_name') || isValueNull('last_name') || isValueNull('email') || isValueNull('phone') || isValueNull('company')
		|| isValueNull('00N50000001kxbM') || isValueNull('00N50000001kxbH')){
	alert('Please fill in all fields marked with *');
	return;
  }

  frm.submit();
}

function isValueNull(field){
  var frm=document;
  if(frm.getElementById(field).value == undefined || frm.getElementById(field).value == ""){
	return true;
  }
  else{
	return false;
  }
}

function autofitIframe(id){
if (!window.opera && !document.mimeType && document.all && document.getElementById){
parent.parent.document.getElementById(id).style.height=this.document.body.offsetHeight+40+"px";
}
else if(document.getElementById) {
parent.parent.document.getElementById(id).style.height=this.document.body.scrollHeight+40+"px"
}
}