CoccoPediaLinker = 1; //on by default can be turned off by add CoccoPediaLinker=0; to each page


function doHighlight(bodyText, searchTerm, highlightStartTag, highlightEndTag) 
{
  // the highlightStartTag and highlightEndTag parameters are optional
  if ((!highlightStartTag) || (!highlightEndTag)) {
    highlightStartTag = "<font style='color:blue; background-color:yellow;'>";
    highlightEndTag = "</font>";
  }
  
  var newText = "";
  var i = -1;
  var lcSearchTerm = searchTerm.toLowerCase();
  var lcBodyText = bodyText.toLowerCase();
    
  while (bodyText.length > 0) {
    i = lcBodyText.indexOf(lcSearchTerm, i+1);
    if (i < 0) {
      newText += bodyText;
      bodyText = "";
    } else {
      // skip attributes of an html tag
      if (bodyText.lastIndexOf(">", i) >= bodyText.lastIndexOf("<", i)) {
	//if already within a link, don't touch it
	if((bodyText.indexOf("</a>", i)!=parseInt(i+lcSearchTerm.length)) && (bodyText.indexOf("</A>", i)!=parseInt(i+lcSearchTerm.length))){
	        // skip anything inside a <script> block
	        if (lcBodyText.lastIndexOf("/script>", i) >= lcBodyText.lastIndexOf("<script", i)) {
	          newText += bodyText.substring(0, i) + highlightStartTag + bodyText.substr(i, searchTerm.length) + highlightEndTag;
	          bodyText = bodyText.substr(i + searchTerm.length);
	          lcBodyText = bodyText.toLowerCase();
	          i = -1;
		}
        }
      }
    }
  }
  
  return newText;
}


function highlightSearchTerms(searchText,  highlightStartTag, highlightEndTag)
{
 
  searchArray = searchText.split(" ");

  if (!document.body || typeof(document.body.innerHTML) == "undefined") {
    return false;
  }
  
  var bodyText = document.body.innerHTML;
  for (var i = 0; i < searchArray.length; i++) {
	   searchArray[i]=replaceAll(searchArray[i],":SPACE:"," ");
	   highlightStartTag = "<a href='http://bioinfo.csusm.edu/CoccoPedia/" + replaceAll(searchArray[i]," ", "_") + "' style='border-bottom: 1px dashed red;text-decoration: none' target=_blank onmouseover=\"ShowPopup(event,'" + replaceAll(searchArray[i]," ", "_")  + "')\" onmouseout='HidePopup()'>";
	   highlightEndTag = "</a>";
           bodyText = doHighlight(bodyText, searchArray[i], highlightStartTag, highlightEndTag);
  }
  
  document.body.innerHTML = bodyText;
  return true;
}


function StartCoccoPediaLinker()
{

  if(CoccoPediaLinker){
	  return highlightSearchTerms("Trim_Est_Sequence Trim:SPACE:Est:SPACE:Sequence Coccolithophorids Emiliana_Huxleyi Emiliana:SPACE:Huxleyi CloVector CloId Library Clone Consensus Blast LibId LibDateConst LibGrowthCond LibInstitu EstId EstDirection EstRawSeq EstRawNumOfBases EstTrimmedSeq EstTrimmedNumOfBases EstDateSequenced EstDateAdded EstComment ConId ConSeq ConNumOfBases ConType BlaHitName BlaDesc BalHspRank BlaHspLength BlaGap BlaHspScore BlaHspBits BlaPrecentIden SubId SubName SubEmail SubPassword SubPhone SubInstitution SubLabName Privacy_policy Privacy:SPACE:policy Site_support Site:SPACE:support General_disclaimer General:SPACE:disclaimer Community_Portal Community:SPACE:Portal Editing Copyrights 207.234.145.43 Community_Portal Community:SPACE:Portal BalHspRank/ EST Main_Page Main:SPACE:Page Pedia/index.php Est_ID Est:SPACE:ID Raw_Est_Sequence Raw:SPACE:Est:SPACE:Sequence Gene_Description Gene:SPACE:Description Blast_Hit_Name Blast:SPACE:Hit:SPACE:Name Submitter_Name Submitter:SPACE:Name Submitter BlaE_value BlaE:SPACE:value Zocor BalHspRank/ EstTrimmedNumOfBases BalHspRank SubPassword CloId ConId LibGrowthCond BlaE_value BlaE:SPACE:value Penis_Growth_Pills Penis:SPACE:Growth:SPACE:Pills ConSeq Current_events Current:SPACE:events SubLabName SubId SubEmail SubPassword/CoccoPedia/Talk:SubPassword/ ConNumOfBases ConId/ EstComment EST EstDirection ConType BlaE_value/ BlaE:SPACE:value/ Index.php/ Index.php/Herbal_Phentermine Index.php/Herbal:SPACE:Phentermine Index.php/Herbal_Phentermine Index.php/Herbal:SPACE:Phentermine Main_Page Main:SPACE:Page Herbal_Phentermine Herbal:SPACE:Phentermine Index.php/ SubId/ Copyrights Herbal_Phentermine Herbal:SPACE:Phentermine General_disclaimer General:SPACE:disclaimer Community Site_supp Site:SPACE:supp General_d General:SPACE:d Privacy_p Privacy:SPACE:p SubEmail/ SubEmail/CoccoPedia/Talk:SubEmail/ Main_Page/ Main:SPACE:Page/ ,_http://privaty-web-surfing.yourplacenew.com/play-surfing-games.html_play_surfing_games,_681516,_http://annetteirwin.1gb.in/alexa-ve6e/skydiving-wallpaper.html_skydiving_wallpaper,_% ,:SPACE:http://privaty-web-surfing.yourplacenew.com/play-surfing-games.html:SPACE:play:SPACE:surfing:SPACE:games,:SPACE:681516,:SPACE:http://annetteirwin.1gb.in/alexa-ve6e/skydiving-wallpaper.html:SPACE:skydiving:SPACE:wallpaper,:SPACE:% 85.255.120.83 General_disclaimer/ General:SPACE:disclaimer/ LibId ,_http://ceoui.cn/brand/brand-new-second-hand.html_brand_new_second_hand,_: ,:SPACE:http://ceoui.cn/brand/brand-new-second-hand.html:SPACE:brand:SPACE:new:SPACE:second:SPACE:hand,:SPACE:: CloId/ 195.54.209.151 121.240.129.100 91.74.160.18 200.142.126.126 Main_Page/index.php Main:SPACE:Page/index.php IP_address IP:SPACE:address 82.103.133.33 62.193.226.136 Zocor Subemail Estcomment Community_portal Community:SPACE:portal Copyright Estcomment Estcomment/ Contents SubPassword/ 62.193.226.136 ConType/ Admin");
  }
}

function replaceAll( str, from, to ) {
    var idx = str.indexOf( from );


    while ( idx > -1 ) {
        str = str.replace( from, to );
        idx = str.indexOf( from );
    }

    return str;
}