anchor.diff:  <%@ page import="org.mskcc.cbio.portal.oncoPrintSpecLanguage.OncoPrintSpecification" %>
   <%@ page import="org.mskcc.cbio.portal.oncoPrintSpecLanguage.Utilities" %>
   <%@ page import="org.mskcc.cbio.portal.model.CancerStudy" %>
  -<%@ page import="org.mskcc.cbio.portal.model.CaseList" %>
  +<%@ page import="org.mskcc.cbio.portal.model.PatientList" %>
   <%@ page import="org.mskcc.cbio.portal.model.GeneticProfile" %>
   <%@ page import="org.mskcc.cbio.portal.model.GeneticAlterationType" %>
   <%@ page import="org.mskcc.cbio.portal.model.Patient" %>
  
positive.code:             var _geneList = '<%=StringUtils.join(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes(), " ")%>';
              return _geneList.split(/\s+/);    //Gene Id list without onco query language
          },
          getCaseSetId: function() { return '<%= caseSetId %>';},  //Id for user chosen standard case set
          getCaseSetName: function() { return '<%= caseSetName %>'},  //Name for user chose standard case set
          getCaseIdsKey: function() { return '<%= caseIdsKey %>'; },   //A key arrsigned to use build case set
          getCases: function() { return '<%= cases %>'; }, // list of queried case ids
          getOqlString: (function() {     // raw gene list (as it is entered by the user, it may contain onco query language)
              var oql = '<%=oql%>'
                      .replace("&gt;", ">", "gm")
  
negative.code:     String genes = (String) request.getAttribute(QueryBuilder.RAW_GENE_STR);
      genes = StringEscapeUtils.escapeJavaScript(genes);
  
      //Info about Patient Set(s)/Patients
      ArrayList<PatientList> patientSets = (ArrayList<PatientList>)request.getAttribute(QueryBuilder.CASE_SETS_INTERNAL);
      ArrayList<String> mergedPatientList = mergedProfile.getCaseIdList();
      int mergedPatientListSize = mergedPatientList.size();
      String patientSetId = (String) request.getAttribute(QueryBuilder.CASE_SET_ID);
      String patientSetName = "";
      for (PatientList patientSet:  patientSets) {
          if (patientSetId.equals(patientSet.getStableId())) {
              patientSetName = patientSet.getName();
          }
      }
      String patients = (String) request.getAttribute(QueryBuilder.SET_OF_CASE_IDS);
      //cases = xssUtil.getCleanerInput(cases);
      String patientIdsKey = (String) request.getAttribute(QueryBuilder.CASE_IDS_KEY);
      //caseIdsKey = xssUtil.getCleanerInput(caseIdsKey);
  
      //Clinical Data
  