anchor.diff:  <%@page import="org.bbop.apollo.web.config.ServerConfiguration.DataAdapterConfiguration"%>
   <%@page import="org.bbop.apollo.web.config.ServerConfiguration.DataAdapterGroupConfiguration"%>
   <%@ page import="org.bbop.apollo.web.config.ServerConfiguration"%>
  +<%@ page import="org.bbop.apollo.web.config.ServerConfiguration.UserDatabaseConfiguration"%>
   <%@ page import="org.bbop.apollo.web.user.UserManager"%>
   <%@ page import="org.bbop.apollo.web.user.Permission"%>
   
  
positive.code: 
  function initialize_config_settings() {
  	$("#datastore_directory").attr("value","<% out.print(serverConfig.getDataStoreDirectory()); %>");
  	$('#webapollo_config_form').submit(function(){
  		serverConfig.setDataStoreDirectory($("#datastore_directory").text());
  	});
  	
  
  	$("#user_database").attr("value","<% out.print(serverConfig.getUserDatabase()); %>");
  }
  
  
  
negative.code: <div id="login_dialog" title="Login">
  </div>
  
  <%
  if ("POST".equalsIgnoreCase(request.getMethod())) {
      // Form was submitted.
      out.println("<p>Settings saved</p>");
      
  	serverConfig.setDataStoreDirectory(request.getParameter("datastore_directory"));
  	serverConfig.setGBOLMappingFile(request.getParameter("mapping_file"));
  	serverConfig.setDefaultMinimumIntronSize(Integer.parseInt(request.getParameter("minimum_intron_size")));
  	serverConfig.setHistorySize(Integer.parseInt(request.getParameter("history_size")));
  	serverConfig.setOverlapperClass(request.getParameter("overlapper_class"));
  	serverConfig.setUseCDS(Boolean.parseBoolean(request.getParameter("use_cds_for_new_transcripts")));
  	serverConfig.setTrackNameComparator(request.getParameter("track_name_comparator"));
  	
  	/*ServerConfiguration.UserDatabaseConfiguration udc=
  			serverConfig.new UserDatabaseConfiguration(
  			request.getParameter("database_driver"),
  			request.getParameter("database_url"),
  			request.getParameter("database_username"),
  			request.getParameter("database_password"));
  	
  	serverConfig.setUserDatabase(udc);*/
  	
  }
  %>
  
  <p>Basic configuration</p>
  
  
  <form id="webapollo_config_form">
  <fieldset class="formLayout">
  
  <label>GBOL Mapping file:
  <input type="text" id="mapping_file"></input> </label>
  
  <label>Annotations data directory:
  <input type="text" id="datastore_directory"></input> </label>
  
  <label>Minimum intron size:
  <input type="text" id="minimum_intron_size"></input> </label>
  
  
  <label>History tracking size:
  <input type="text" id="history_size"></input> </label>
  
  
  <label>Overlapper class:
  <input type="text" id="overlapper_class"></input> </label>
  
  <label>Track name comparator:
  <input type="text" id="track_name_comparator"></input> </label>
  
  <label>Use existing CDS when creating new transcript:
  <input type="text" id="use_cds_for_new_transcripts"></input> </label>
  
  
  </fieldset>
  <br />
  <br />
  
  <p>User database configuration</p>
  <fieldset class="formLayout">
  
  <label>Username:
  <input type="text" id="database_username"></input> </label>
  
  <label>Password:
  <input type="password" id="database_password"></input> </label>
  
  <label>Driver:
  <input type="text" id="database_driver"></input> </label>
  
  <label>URL:
  <input type="text" id="database_url"></input> </label>
  
  </fieldset>
  <br />
  <input type="submit" value="Submit"></input>
  </form>
  
  