anchor.diff:  </tr>
   
   <%
  -				}
  -			}
  -			%>
  +
  +                    }
  +                }
  +                %>
   
   </tr>
   <tr>
       <td colspan="2" bgcolor="#eeeeee"><B>Quantitation</B></td>
   </tr>
   <%
  -		if( ee.getAnalyses().size()==0) {
  -			out.print("<tr><td colspan='2'>No analysis for this experiment</td></tr>");
  -		}
  -		else{
  -			out.print("<tr><td colspan='2'>"+ ee.getAnalyses().size()+ "</td></tr>");
  -		}
  -		%>
  +if ( ee.getAnalyses().size() == 0 ) {
  +                    out.print( "<tr><td colspan='2'>No analysis for this experiment</td></tr>" );
  +                } else {
  +                    out.print( "<tr><td colspan='2'>" + ee.getAnalyses().size() + "</td></tr>" );
  +                }
  +
  +                %>
   <tr>
       <td colspan="2" bgcolor="#eeeeee"><B>DesignElement Data Vectors</B></td>
   </tr>
   <%
  -		
  -		if( ee.getDesignElementDataVectors().size()==0){
  -			out.print("<tr><td colspan='2'>No DesignElementDataVectors for this experiment</td></tr>");
  -		}
  -		else{
  -			for(Iterator iter=ee.getDesignElementDataVectors().iterator(); iter.hasNext(); ){
  -				DesignElementDataVector ddv = (DesignElementDataVector) iter.next();
  -				out.print( "<tr><td>" + ddv.getDesignElement().getName()  + "</td><td>");
  -				out.print ("Quant: " + ddv.getQuantitationType().getName() + "</td></tr>");
  -			}	
  -		}
  -		%>
  +if ( ee.getDesignElementDataVectors().size() == 0 ) {
  +                    out.print( "<tr><td colspan='2'>No DesignElementDataVectors for this experiment</td></tr>" );
  +                } else {
  +                    for ( Iterator iter = ee.getDesignElementDataVectors().iterator(); iter.hasNext(); ) {
  +                        DesignElementDataVector ddv = ( DesignElementDataVector ) iter.next();
  +                        out.print( "<tr><td>" + ddv.getDesignElement().getName() + "</td><td>" );
  +                        out.print( "Quant: " + ddv.getQuantitationType().getName() + "</td></tr>" );
  +                    }
  +                }
  +                %>
   <tr>
       <td colspan="2" bgcolor="#eeeeee"><b>Bio Assays</b></td>
   </tr>
   <%
  -		if( ee.getBioAssays().size()==0){
  -			out.print("<tr><td colspan='2'>No BioAssays for this experiment</td></tr>");
  -		}
  -		else{
  -			for(Iterator iter=ee.getBioAssays().iterator(); iter.hasNext(); ){
  -				
  -				BioAssay ba = (BioAssay) iter.next();
  -				
  -				out.print( "<tr><td valign='top'>" + ba.getName() + "</td><td>");
  -				String baAcc="(No Accession)";
  -				String baDesc="(No Description)";
  -				if( ba.getAccession() != null ){
  -					baAcc = ba.getAccession().getAccession();
  -				}
  -				out.print(baAcc + " " + baDesc );
  -				if( ba.getBioAssayFactorValues().size()==0){
  -					out.print("No factor values<BR>");
  -				}
  -				else{
  -					out.print("Factor values:<BR>" );
  -					for(Iterator iterF=ba.getBioAssayFactorValues().iterator(); iterF.hasNext(); ){
  -						FactorValue fv = (FactorValue) iterF.next();
  -						String factorValue="Unknown Value";
  -						String factorMeasurement="";
  -						if(fv.getValue() != null){
  -							factorValue = fv.getValue().getValue();
  -						}
  -						if( fv.getMeasurement()!=null ){
  -							factorMeasurement = "(" + fv.getMeasurement().getValue() + ")";
  -						}
  -						out.print(": " + factorValue + " " + factorMeasurement );
  -						
  -					}
  -				}
  -				if( ba.getArrayDesignsUsed().size()==0){
  -					out.print("No array designs<BR>");
  -				}
  -				else{
  -					out.print("<b>Array designs</b>:<BR>" );
  -					for(Iterator iterD=ba.getArrayDesignsUsed().iterator(); iterD.hasNext(); ){
  -						ArrayDesign ad = (ArrayDesign) iterD.next();
  -						String adDesc="(no description)";
  -						String adName = "(No name)";
  -						if( ad.getDescription() != null )
  -							adDesc = ad.getDescription();
  -						if( ad.getName() != null )
  -							adName = ad.getName();
  -						
  -						out.print( adName + " (" + ad.getDesignElements().size() + " elements)<br>" + adDesc);
  -						if( ad.getDesignProvider() == null )
  -							out.print("Unknown provider");
  -						else
  -							out.print(ad.getDesignProvider().getName());
  -						
  -					}
  -				}
  -				out.print("</td></tr>");
  -				out.print("<tr><td colspan='2'><hr></td></tr>");
  -			}
  -				
  -		}
  -		%>
  +if ( ee.getBioAssays().size() == 0 ) {
  +                    out.print( "<tr><td colspan='2'>No BioAssays for this experiment</td></tr>" );
  +                } else {
  +                    for ( Iterator iter = ee.getBioAssays().iterator(); iter.hasNext(); ) {
  +
  +                        BioAssay ba = ( BioAssay ) iter.next();
  +
  +                        out.print( "<tr><td valign='top'>" + ba.getName() + "</td><td>" );
  +                        String baAcc = "(No Accession)";
  +                        String baDesc = "(No Description)";
  +                        if ( ba.getAccession() != null ) {
  +                            baAcc = ba.getAccession().getAccession();
  +                        }
  +                        out.print( baAcc + " " + baDesc );
  +                        if ( ba.getFactorValues().size() == 0 ) {
  +                            out.print( "No factor values<BR>" );
  +                        } else {
  +                            out.print( "Factor values:<BR>" );
  +                            for ( Iterator iterF = ba.getFactorValues().iterator(); iterF.hasNext(); ) {
  +                                FactorValue fv = ( FactorValue ) iterF.next();
  +                                String factorValue = "Unknown Value";
  +                                String factorMeasurement = "";
  +                                if ( fv.getValue() != null ) {
  +                                    factorValue = fv.getValue().getValue();
  +                                }
  +                                if ( fv.getMeasurement() != null ) {
  +                                    factorMeasurement = "(" + fv.getMeasurement().getValue() + ")";
  +                                }
  +                                out.print( ": " + factorValue + " " + factorMeasurement );
  +
  +                            }
  +                        }
  +                        if ( ba.getArrayDesignsUsed().size() == 0 ) {
  +                            out.print( "No array designs<BR>" );
  +                        } else {
  +                            out.print( "<b>Array designs</b>:<BR>" );
  +                            for ( Iterator iterD = ba.getArrayDesignsUsed().iterator(); iterD.hasNext(); ) {
  +                                ArrayDesign ad = ( ArrayDesign ) iterD.next();
  +                                String adDesc = "(no description)";
  +                                String adName = "(No name)";
  +                                if ( ad.getDescription() != null ) adDesc = ad.getDescription();
  +                                if ( ad.getName() != null ) adName = ad.getName();
  +
  +                                out.print( adName + " (" + ad.getDesignElements().size() + " elements)<br>" + adDesc );
  +                                if ( ad.getDesignProvider() == null )
  +                                    out.print( "Unknown provider" );
  +                                else
  +                                    out.print( ad.getDesignProvider().getName() );
  +
  +                            }
  +                        }
  +                        out.print( "</td></tr>" );
  +                        out.print( "<tr><td colspan='2'><hr></td></tr>" );
  +                    }
  +
  +                }
  +
  +            %>
   <%-- </table> --%>
  -<%	
  -	}
  -}
  -else
  -	out.print("No experiment with that ID was found.<BR>");
  +<%}
  +        } else
  +            out.print( "No experiment with that ID was found.<BR>" );
   %>
   
   </body>
  
positive.code: <tr>
      <td valign='top'>Design Types:</td>
      <td><%
  						for(Iterator iterTypes=ed.getTypes().iterator(); iterTypes.hasNext(); ){
  							OntologyEntry oe = (OntologyEntry) iterTypes.next();
  							out.print(oe.getValue() + "<br>");	
  						}
  						%></td>
  </tr>
  <tr>
      <td valign='top'>Factors</td>
      <td><%
  						String categoryName="";
  						String factorList="";
  						if( ed.getExperimentalFactors().size()==0 )
  							out.print("No Factors for this experiment");
  						else{
  							for(Iterator iterFac=ed.getExperimentalFactors().iterator(); iterFac.hasNext(); ){
  								categoryName="";
  								factorList="";
  								String factorValue="";
  								String factorMeasurement="";
  								ExperimentalFactor fac = (ExperimentalFactor) iterFac.next();
  								OntologyEntry category = fac.getCategory();
  								if( category==null)
  									categoryName="Unknown";
  								else
  									categoryName=category.getValue();
  								for(Iterator iterFacValues=fac.getFactorValues().iterator(); iterFacValues.hasNext(); ){
  									FactorValue fv = (FactorValue) iterFacValues.next();	
  									OntologyEntry fvValue = fv.getValue();
  									if(fvValue==null)
  										factorValue="Unknown Value";
  									else
  										factorValue = fvValue.getValue();
  									if(fv.getMeasurement()==null)
  										factorMeasurement="";
  									else
  										factorMeasurement = fv.getMeasurement().getValue();
  									factorList = factorList + " (" + factorValue + ") " + factorMeasurement + "<br>";
  								}						
  							}
  						}
  						
  						%>
      <table>
          <tr>
              <td valign='top'><b><%=categoryName%></b>:</td>
  
negative.code:     ID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</td>
      <td bgcolor="white"><input type="text" name="primaryPubmed"
          id="primaryPubmed" value="<%=pubmedAcc%>"> <%
  
                  if ( pubmedAcc != "" ) {%>
      &nbsp;<a
          href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=<%=pubmedAcc%>">View
      Article</a> <%
  
                  }
                  %></td>
  </tr>
  <tr>
      <td valign="top" bgcolor="white">Description:</td>
  