anchor.diff: -<%@ taglib uri="http://java.sun.com/jsf/html" prefix="h" %>
  -<%@ taglib uri="http://java.sun.com/jsf/core" prefix="f" %>
  -<%@ page import="java.util.List" %>
  -<%@ page import="java.util.Date" %>
  -<%@ page import="java.text.SimpleDateFormat" %>
  +<%@ taglib uri="http://java.sun.com/jsf/html" prefix="h"%>
  +<%@ taglib uri="http://java.sun.com/jsf/core" prefix="f"%>
  +<%@ page import="java.util.List"%>
  +<%@ page import="java.util.Date"%>
  +<%@ page import="java.text.SimpleDateFormat"%>
   <%@ page import="java.util.Vector"%>
   <%@ page import="java.util.HashSet"%>
   <%@ page import="java.util.HashMap"%>
   <%@ page import="java.util.ArrayList"%>
   <%@ page import="java.util.Set"%>
   <%@ page import="java.util.Iterator"%>
  -<%@ page import="gov.nih.nci.evs.browser.utils.DataUtils" %>
  -<%@ page import="gov.nih.nci.evs.browser.properties.PropertyFileParser" %>
  -<%@ page import="gov.nih.nci.evs.browser.properties.NCItBrowserProperties" %>
  -<%@ page import="gov.nih.nci.evs.browser.bean.DisplayItem" %>
  -<%@ page import="gov.nih.nci.evs.browser.bean.*" %>
  -<%@ page import="gov.nih.nci.evs.browser.utils.*" %>
  -<%@ page import="org.LexGrid.concepts.Concept" %>
  -<%@ page import="org.LexGrid.concepts.Presentation" %>
  -<%@ page import="org.LexGrid.commonTypes.Source" %>
  -<%@ page import="org.LexGrid.commonTypes.EntityDescription" %>
  -<%@ page import="org.LexGrid.commonTypes.Property" %>
  -<%@ page import="org.LexGrid.commonTypes.PropertyQualifier" %>
  -<%@ page import="org.LexGrid.concepts.Presentation" %>
  -<%@ page import="org.LexGrid.commonTypes.Source" %>
  -<%@ page import="org.LexGrid.commonTypes.EntityDescription" %>
  -<%@ page import="org.LexGrid.commonTypes.Property" %>
  -<%@ page import="org.LexGrid.commonTypes.PropertyQualifier" %>
  -<%@ page import="gov.nih.nci.evs.browser.common.Constants" %>
  +<%@ page import="gov.nih.nci.evs.browser.utils.DataUtils"%>
  +<%@ page import="gov.nih.nci.evs.browser.properties.PropertyFileParser"%>
  +<%@ page
  +	import="gov.nih.nci.evs.browser.properties.NCItBrowserProperties"%>
  +<%@ page import="gov.nih.nci.evs.browser.bean.DisplayItem"%>
  +<%@ page import="gov.nih.nci.evs.browser.bean.*"%>
  +<%@ page import="gov.nih.nci.evs.browser.utils.*"%>
  +<%@ page import="org.LexGrid.concepts.Concept"%>
  +<%@ page import="org.LexGrid.concepts.Presentation"%>
  +<%@ page import="org.LexGrid.commonTypes.Source"%>
  +<%@ page import="org.LexGrid.commonTypes.EntityDescription"%>
  +<%@ page import="org.LexGrid.commonTypes.Property"%>
  +<%@ page import="org.LexGrid.commonTypes.PropertyQualifier"%>
  +<%@ page import="org.LexGrid.concepts.Presentation"%>
  +<%@ page import="org.LexGrid.commonTypes.Source"%>
  +<%@ page import="org.LexGrid.commonTypes.EntityDescription"%>
  +<%@ page import="org.LexGrid.commonTypes.Property"%>
  +<%@ page import="org.LexGrid.commonTypes.PropertyQualifier"%>
  +<%@ page import="gov.nih.nci.evs.browser.common.Constants"%>
   <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
   <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
   <head>
  -  <title>NCI Thesaurus</title>
  -  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
  -  <link rel="stylesheet" type="text/css" href="<%= request.getContextPath() %>/css/styleSheet.css" />
  -  <script type="text/javascript" src="<%= request.getContextPath() %>/js/script.js"></script>
  -  <script type="text/javascript" src="<%= request.getContextPath() %>/js/search.js"></script>
  -  <script type="text/javascript" src="<%= request.getContextPath() %>/js/dropdown.js"></script>
  +<title>NCI Thesaurus</title>
  +<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
  +<link rel="stylesheet" type="text/css"
  +	href="<%= request.getContextPath() %>/css/styleSheet.css" />
  +<script type="text/javascript"
  +	src="<%= request.getContextPath() %>/js/script.js"></script>
  +<script type="text/javascript"
  +	src="<%= request.getContextPath() %>/js/search.js"></script>
  +<script type="text/javascript"
  +	src="<%= request.getContextPath() %>/js/dropdown.js"></script>
   </head>
   <body leftmargin="0" topmargin="0" marginwidth="0" marginheight="0">
   
  -  <f:view>
  -    <%@ include file="/pages/templates/header.xhtml" %>
  -    <div class="center-page">
  -	      <%@ include file="/pages/templates/sub-header.xhtml" %>
  -	      
  -<table>
  -    <tr>
  -        <td>
  -
  -    <div class="banner"><a href="<%=basePath%>"><img src="<%=basePath%>/images/evs_bioportal_logo.jpg" width="383" height="82" alt="Thesaurus Browser Logo" border="0"/></a></div>
  -
  -        </td>
  -        <td>
  -
  -        <!-- Search box -->
  -        <div class="searchbox-top"><img src="<%=basePath%>/images/searchbox-top.gif" width="352" height="2" alt="SearchBox Top" /></div>
  -	
  -		  <%
  +<f:view>
  +	<%@ include file="/pages/templates/header.xhtml"%>
  +	<div class="center-page"><%@ include
  +		file="/pages/templates/sub-header.xhtml"%>
  +
  +	<table>
  +		<tr>
  +			<td>
  +
  +			<div class="banner"><a href="<%=basePath%>"><img
  +				src="<%=basePath%>/images/evs_bioportal_logo.jpg" width="383"
  +				height="82" alt="Thesaurus Browser Logo" border="0" /></a></div>
  +
  +			</td>
  +			<td><!-- Search box -->
  +			<div class="searchbox-top"><img
  +				src="<%=basePath%>/images/searchbox-top.gif" width="352" height="2"
  +				alt="SearchBox Top" /></div>
  +
  +			<%
   		    String match_text = gov.nih.nci.evs.browser.utils.HTTPUtils.cleanXSS((String) request.getSession().getAttribute("matchText"));
   		    if (match_text == null) match_text = "";
   		  %>
  -	
  -	
  -<FORM NAME="searchTerm" METHOD="POST" CLASS="search-form" >
  -		  
  -		  
  -		  <input CLASS="searchbox-input"
  -		    name="matchText"
  -		    value="<%=match_text%>"
  -		    onFocus="active = true" onBlur="active = false" onkeypress="return submitEnter('search',event)"
  -		  />
  -		  <h:commandButton
  -		    id="search"
  -		    value="Search"
  -		    action="#{userSessionBean.multipleSearchAction}"
  -		    image="#{facesContext.externalContext.requestContextPath}/images/search.gif"
  -		    alt="Search">
  -		  </h:commandButton>
  -		  <h:outputLink value="#{facesContext.externalContext.requestContextPath}/pages/help.jsf#searchhelp">
  -		    <h:graphicImage value="/images/search-help.gif" style="border-width:0;"/>
  -		  </h:outputLink>
  -		  <%
  +
  +
  +			<FORM NAME="searchTerm" METHOD="POST" CLASS="search-form"><input
  +				CLASS="searchbox-input" name="matchText" value="<%=match_text%>"
  +				onFocus="active = true" onBlur="active = false"
  +				onkeypress="return submitEnter('search',event)" /> <h:commandButton
  +				id="search" value="Search"
  +				action="#{userSessionBean.multipleSearchAction}"
  +				image="#{facesContext.externalContext.requestContextPath}/images/search.gif"
  +				alt="Search">
  +			</h:commandButton> <h:outputLink
  +				value="#{facesContext.externalContext.requestContextPath}/pages/help.jsf#searchhelp">
  +				<h:graphicImage value="/images/search-help.gif"
  +					style="border-width:0;" />
  +			</h:outputLink> <%
   		    String algorithm = (String) request.getSession().getAttribute("selectedAlgorithm");
   		    String check_e = "", check_s = "" , check_c ="";
   		    if (algorithm == null || algorithm.compareTo("exactMatch") == 0)
  
positive.code: 
                                                      if ( scheme.compareTo("NCI Thesaurus") == 0) {
                                                      %>
  							    <li>
  							    <%
  							    if (ontologiesToSearchOn != null && ontologiesToSearchOn.indexOf(label2) != -1) {
  							    %>
  							        <input type="checkbox" name="ontology_list" value="<%=label%>" checked/>
  							    <%    
  							    } else {
  							    %>
  							        <input type="checkbox" name="ontology_list" value="<%=label%>" />
  							    <%    
  							    }
  							    %>
  							    <a href="<%= request.getContextPath() %>"><%=label%></a>
  							    </li>  
  					            <%		    
                                                      } else if ( scheme.compareTo("NCI MetaThesaurus") == 0) {
                                                          String ncimurl = NCItBrowserProperties.getNCIM_URL();
                                                      %>
  							    <li>
  							    <%
  							    if (ontologiesToSearchOn != null && ontologiesToSearchOn.indexOf(label2) != -1) {
  							    %>
  							        <input type="checkbox" name="ontology_list" value="<%=label%>" checked/>
  							    <%    
  							    } else {
  							    %>
  							        <input type="checkbox" name="ontology_list" value="<%=label%>" />
  							    <%    
  							    }
  							    %>							    
  							    <a href="http://ncim.nci.nih.gov"><%=label%></a>
  							    </li>  
  					            <%		    
                                                      } else {
                                                      %>
  							    <li>
  							    <%
  							    if (ontologiesToSearchOn != null && ontologiesToSearchOn.indexOf(label2) != -1) {
  							    %>
  							        <input type="checkbox" name="ontology_list" value="<%=label%>" checked/>
  							    <%    
  							    } else {
  							    %>
  							        <input type="checkbox" name="ontology_list" value="<%=label%>" />
  							    <%    
  							    }
  							    %>								    
  							    <a href="<%= request.getContextPath() %>/pages/vocabulary.jsf?dictionary=<%=http_label%>&scheme=<%=http_scheme%>&version=<%=http_version%>" alt="<%=label%>"><%=label%></a>
  							    </li>
  				                    <%
  				                    }
  						}
  					    %>	
   					    </ol>
  					
  					</td>
  					
  				     </tr>
  				     <tr>
  				        <td>
  
  
  <img src="<%= request.getContextPath() %>/images/selectAll.gif" name="selectAll" alt="selectAll" onClick="checkAll(document.searchTerm.ontology_list)"/>
  &nbsp;&nbsp;
  <img src="<%= request.getContextPath() %>/images/reset.gif" name="reset" alt="reset" onClick="uncheckAll(document.searchTerm.ontology_list)"/>
  
  &nbsp;&nbsp;
  		  <h:commandButton
  		    id="search"
  		    value="Search"
  		    action="#{userSessionBean.multipleSearchAction}"
  		    image="#{facesContext.externalContext.requestContextPath}/images/search.gif"
  		    alt="Search">
  		  </h:commandButton>
  		  
                                          </td>
                                       </tr>   
  				  </table>
  				  
  			      </div>
  
  			      <%@ include file="/pages/templates/nciFooter.html" %>
  			      
  			</div>
  			<!-- end Page content -->
  			
  </div></form>
  
  	      </div>
  		      
  	      <div class="mainbox-bottom"><img src="<%=basePath%>/images/mainbox-bottom.gif" width="745" height="5" alt="Mainbox Bottom" />
  	      </div>
  	      <!-- end Main box -->
      </div>
      
    </f:view>
  </body>
  </html>
negative.code: 		    else
  		      check_c = "checked";
  		  %>
  
  			<div class="textbody"><input type="radio" name="algorithm"
  				value="exactMatch" alt="Exact Match" <%=check_e%>>Exact
  			Match&nbsp; <input type="radio" name="algorithm" value="startsWith"
  				alt="Begins With" <%=check_s%>>Begins With&nbsp; <input
  				type="radio" name="algorithm" value="contains" alt="Containts"
  				<%=check_c%>>Contains&nbsp;</div>
  
  			<div class="searchbox-bottom"><img
  				src="<%=basePath%>/images/searchbox-bottom.gif" width="352"
  				height="2" alt="SearchBox Bottom" /></div>
  
  			<!-- end Search box --> <!-- Global Navigation --> <%@ include
  				file="/pages/templates/menuBar2.xhtml"%> <!-- end Global Navigation -->
  			</td>
  
  		</tr>
  
  	</table>
  
  	<!-- end Thesaurus, banner search area --> <!-- Quick links bar --> <%@ include
  		file="/pages/templates/quickLink.xhtml"%> <!-- end Quick links bar -->
  
  	<!-- Page content -->
  	<div class="pagecontent">
  
  	<div class="tabTableContentContainer">
  
  	<p class="textbody">&nbsp;Select NCI hosted terminologies to
  	search, or click on a source name to go to its browser home page.</p>
  	<table class="datatable">
  		<tr>
  
  			<%
  					    List ontology_list = DataUtils.getOntologyList();
  					    if (ontology_list == null) System.out.println("??????????? ontology_list == null");
  					    int num_vocabularies = ontology_list.size();
  