anchor.diff:      String genes = (String) request.getAttribute(QueryBuilder.RAW_GENE_STR);
       genes = StringEscapeUtils.escapeJavaScript(genes);
   
  -    //Info about Case Set(s)/Cases
  -    ArrayList<CaseList> caseSets = (ArrayList<CaseList>)request.getAttribute(QueryBuilder.CASE_SETS_INTERNAL);
  -    ArrayList<String> mergedCaseList = mergedProfile.getCaseIdList();
  -    int mergedCaseListSize = mergedCaseList.size();
  -    String caseSetId = (String) request.getAttribute(QueryBuilder.CASE_SET_ID);
  -    String caseSetName = "";
  -    for (CaseList caseSet:  caseSets) {
  -        if (caseSetId.equals(caseSet.getStableId())) {
  -            caseSetName = caseSet.getName();
  -        }
  -    }
  -    String cases = (String) request.getAttribute(QueryBuilder.SET_OF_CASE_IDS);
  +    //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 caseIdsKey = (String) request.getAttribute(QueryBuilder.CASE_IDS_KEY);
  +    String patientIdsKey = (String) request.getAttribute(QueryBuilder.CASE_IDS_KEY);
       //caseIdsKey = xssUtil.getCleanerInput(caseIdsKey);
   
       //Clinical Data
  
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: <%@ 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.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" %>
  