Changeset 2490

Timestamp:

Aug 8, 2006, 9:29:35 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

References #127: Experiment explorer

• Added annotations, support for formula columns. Now mostly needs to be cleaned up and documented.
• Fixed another problem with COUNT(DISTINCT) queries.
• Changed stylesheet for forms on view pages

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java (modified) (12 diffs)
• src/core/net/sf/basedb/core/AbstractEntityQuery.java (modified) (1 diff)
• src/core/net/sf/basedb/core/AbstractQuery.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ItemContext.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Operator.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PropertyFilter.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawDataType.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/query/ExpressionSelect.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/query/Select.java (modified) (1 diff)
• src/core/net/sf/basedb/core/query/Selects.java (modified) (2 diffs)
• www/include/styles/main.css (modified) (2 diffs)
• www/views/experiments/bioassaysets/view_bioassayset.jsp (modified) (1 diff)
• www/views/experiments/explorer/search/index.jsp (modified) (2 diffs)
• www/views/experiments/explorer/search/list.jsp (modified) (2 diffs)
• www/views/experiments/explorer/view/index.jsp (modified) (2 diffs)
• www/views/experiments/explorer/view/view.jsp (modified) (15 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java

@@ -115 +115 @@
   
   // TODO - fix for use with table listings
-  public static void addFormulaColumns(List<TableColumn> columns, DbControl dc, RawDataType rawDataType, Formula.Type type)
+  public static void addFormulaColumns(List<TableColumn> columns, DbControl dc, RawDataType rawDataType, Formula.Type type, String idPrefix, String titlePrefix)
   {
     ItemQuery<Formula> query = Formula.getQuery(type, rawDataType);
@@ -124 +124 @@
     {
       Formula f = result.next();
-      TableColumn tc = new TableColumn(null, null, f.getFormula(0), Type.FLOAT, f.getName(), f.getDescription());
+      String jepExpression = f.getFormula(0);
+      TableColumn tc = new TableColumn(idPrefix+f.getId(), "="+jepExpression, jepExpression, Type.FLOAT, 
+        titlePrefix + f.getName(), f.getDescription());
       columns.add(tc);
     }

trunk/src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java

@@ -70 +70 @@
   public static final int SPOT_AVG = -2;
   
-  private static final Map<RawDataType, ItemContext> defaultContexts = 
+  private static final ItemContext defaultReporterContext = 
+    Base.createDefaultContext("@externalId", "name,externalId");
+  
+  private static final Map<RawDataType, ItemContext> defaultSpotContexts = 
     new HashMap<RawDataType, ItemContext>();
 
@@ -78 +81 @@
     {
       // Default visible columns are: position, ch1, ch2, ...
-      StringBuilder columns = new StringBuilder("POSITION");
+      StringBuilder columns = new StringBuilder("bioassay,position");
       for (int ch = 1; ch <= rdt.getChannels(); ++ch)
       {
         columns.append(",ch").append(ch);
       }
-      defaultContexts.put(rdt, 
+      defaultSpotContexts.put(rdt, 
         Base.createDefaultContext("POSITION", columns.toString()));
     }
@@ -101 +104 @@
   }
   
-  private static final int CACHE_SIZE = 10;
+  private static final int DEFAULT_CACHE_SIZE = 100;
   
   private final BioAssaySet bioAssaySet;
   private final Map<Short, Integer> bioAssays;
   private int[] reporterIds;
+  private int cacheSize;
   private int firstCachedIndex = 0;
   private int lastCachedIndex = -1;
   private int reporterIndex = 0;
   private int positionIndex = 0;
+  private int matchingReporters = -1;
+  private int annotationTypeId = 0;
   
   private ExperimentExplorer(BioAssaySet bioAssaySet)
@@ -115 +121 @@
     this.bioAssaySet = bioAssaySet;
     this.bioAssays = new HashMap<Short, Integer>();
+    this.cacheSize = DEFAULT_CACHE_SIZE;
     for (BioAssay ba : bioAssaySet.getBioAssays().list(bioAssaySet.getDbControl()))
     {
@@ -121 +128 @@
   }
 
+  public int getCacheSize()
+  {
+    return cacheSize;
+  }
+  
+  public void setCacheSize(int cacheSize)
+  {
+    this.cacheSize = cacheSize;
+  }
+  
   /**
     Get the bioassay set that is currently beeing explored.
@@ -176 +193 @@
   }
   
-  public ItemContext getDefaultContext()
-  {
-    return defaultContexts.get(bioAssaySet.getRawDataType());
+  public ItemContext getDefaultSpotContext()
+  {
+    return defaultSpotContexts.get(bioAssaySet.getRawDataType());
+  }
+
+  public ItemContext getDefaultReporterContext()
+  {
+    return defaultReporterContext;
   }
   
   public ItemContext getAndSetSpotContext(SessionControl sc, PageContext pageContext)
   {
-    ItemContext cc = Base.getAndSetCurrentContext(sc, Item.SPOTDATA, getSubContext(), pageContext, getDefaultContext());
+    ItemContext cc = Base.getAndSetCurrentContext(sc, Item.SPOTDATA, getSubContext(), pageContext, getDefaultSpotContext());
     if (pageContext != null)
     {
@@ -192 +214 @@
   }
   
-  public ItemContext getAndSetReporterContext(SessionControl sc, PageContext pageContext, ItemContext defaultContext)
-  {
-    ItemContext cc = Base.getAndSetCurrentContext(sc, Item.REPORTER, getSubContext(), pageContext, defaultContext);
+  public ItemContext getAndSetReporterContext(SessionControl sc, PageContext pageContext)
+  {
+    ItemContext cc = Base.getAndSetCurrentContext(sc, Item.REPORTER, getSubContext(), pageContext, getDefaultReporterContext());
+    if (pageContext != null)
+    {
+      // Settings may have changes, clear cache
+      firstCachedIndex = 0;
+      lastCachedIndex = -1;
+      matchingReporters = -1;
+    }
     return cc;
   }
@@ -204 +233 @@
   public int getMatchingReporters(DbControl dc)
   {
-    return (int)getReporterQuery(dc, null).count(dc);
+    if (matchingReporters == -1)
+    {
+      matchingReporters = (int)getReporterQuery(dc, null).count(dc);
+    }
+    return matchingReporters;
+  }
+  
+  public int getAnnotationTypeId()
+  {
+    return annotationTypeId;
+  }
+  
+  public void setAnnotationTypeId(int annotationTypeId)
+  {
+    this.annotationTypeId = annotationTypeId;
   }
   
@@ -218 +261 @@
   /**
     Set the index of the currently viewed reporter. If the index is below
-    zero or greater than or equal to {@link #getMatchingReporters()} it is set
+    zero or greater than or equal to {@link #getMatchingReporters(DbControl)} it is set
     to the nearest index.
     @param reporterIndex The new index
@@ -224 +267 @@
   public void setReporterIndex(int reporterIndex)
   {
+    if (reporterIndex >= matchingReporters) reporterIndex = matchingReporters - 1;
     if (reporterIndex < 0) reporterIndex = 0;
-//    if (reporterIndex >= getMatchingReporters()) reporterIndex = getMatchingReporters() - 1;
     this.reporterIndex = reporterIndex;
   }
@@ -237 +280 @@
   public ReporterData getReporter(DbControl dc, int index)
   {
-    if (reporterIds == null)
-    {
-      reporterIds = new int[CACHE_SIZE];
+    if (reporterIds == null || reporterIds.length != cacheSize)
+    {
+      reporterIds = new int[cacheSize];
     }
     
     if (index < firstCachedIndex || index > lastCachedIndex)
     {
-      // The index is outside the cached range, reload another range: index +/- CACHE_SIZE / 2
+      // The index is outside the cached range, reload another range: index +/- (cacheSize / 2)
       BioAssaySet bas = getBioAssaySet(dc);
       
       DynamicSpotQuery reporterQuery = getReporterQuery(dc, null);
       
-      this.firstCachedIndex = Math.max(0, index - CACHE_SIZE / 2);
+      this.firstCachedIndex = Math.max(0, index - cacheSize / 2);
       reporterQuery.setFirstResult(firstCachedIndex);
-      reporterQuery.setMaxResults(CACHE_SIZE);
+      reporterQuery.setMaxResults(cacheSize);
       try
       {
@@ -356 +399 @@
     reporterQuery.joinReporters(JoinType.INNER);
     reporterQuery.setDistinct(true);
-    reporterQuery.select(Dynamic.selectReporter("id"));
-
+    reporterQuery.select(Selects.expression(Dynamic.reporter("id"), "id", true));
+    
     ItemContext cc = dc.getSessionControl().getCurrentContext(Item.REPORTER, getSubContext(), null);
     cc.configureQuery(reporterQuery, selectionList);

trunk/src/core/net/sf/basedb/core/AbstractEntityQuery.java

@@ -153 +153 @@
     this.requiredFilter = QueryRuntimeFilterFactory.getRequiredFilter(itemType);
     this.optionalFilter = optionalFilter;
-    super.selectPermanent(Selects.expression(Hql.alias(itemType.getAlias()), null));
+    super.selectPermanent(Selects.expression(Hql.alias(itemType.getAlias()), null, true));
     this.includes = EnumSet.of(Include.NOT_REMOVED, Include.MINE, Include.IN_PROJECT);
     this.permission = Permission.READ;

trunk/src/core/net/sf/basedb/core/AbstractQuery.java

@@ -687 +687 @@
     for (Select s : selects)
     {
-      ql.append(deliminator);
-      ql.append(dc == null ? s.toString() : s.toQl(this, dc));
-      appended++;
-      deliminator = ", ";
+      if (!isCounting || s.useInDistinctCount())
+      {
+        ql.append(deliminator);
+        ql.append(dc == null ? s.toString() : s.toQl(this, dc));
+        appended++;
+        deliminator = ", ";
+      }
     }
     return appended;

trunk/src/core/net/sf/basedb/core/ItemContext.java

@@ -39 +39 @@
 import net.sf.basedb.core.data.UserData;
 import net.sf.basedb.core.data.ClientData;
+import net.sf.basedb.util.jep.ChannelFunction;
+import net.sf.basedb.util.jep.Jep;
+import net.sf.basedb.util.jep.JepFunction;
+import net.sf.basedb.util.jep.RawFunction;
 
 import java.util.Collection;
@@ -148 +152 @@
   public static final String DEFAULT_NAME = "- default -";
 
+  // For parsing JEP expressions
+  private static final JepFunction ch = new ChannelFunction();
+  private static final JepFunction raw = new RawFunction();
+  
   private final String name;
   private final Item itemType;
@@ -942 +950 @@
       // TODO - implement extra values
     }
+    else if (propertyDef.startsWith("="))
+    {
+      // propertyDef is JEP expression
+      joins.joinRawData |= propertyDef.contains("raw(");
+      e = Jep.formulaToExpression(propertyDef.substring(1), ch, raw);
+    }
     else
     {

trunk/src/core/net/sf/basedb/core/Operator.java

@@ -151 +151 @@
   }
 
+  public String toString()
+  {
+    return symbol;
+  }
+  
   /**
     Get the integer value that is used when storing an operator in the database.

trunk/src/core/net/sf/basedb/core/PropertyFilter.java

@@ -98 +98 @@
     return filter;
   }
+  
+  /*
+    From the Object class
+    -------------------------------------------
+  */
+  public String toString()
+  {
+    return property + " " + operator + " " + value;
+  }
+  // -------------------------------------------
+
   
   /**

trunk/src/core/net/sf/basedb/core/RawDataType.java

@@ -27 +27 @@
 import java.util.HashMap;
 import java.util.Collections;
+
+import net.sf.basedb.core.data.RawData;
 
 /**
@@ -232 +234 @@
     return name;
   }
+  
+  public RawData getRawDataById(DbControl dc, int id)
+    throws ItemNotFoundException, PermissionDeniedException, BaseException
+  {
+    if (!isStoredInDb())
+    {
+      throw new BaseException("Raw data for raw data type '" + this + "' is not stored in the database.");
+    }
+    RawData rd = HibernateUtil.loadData(dc.getStatelessSession(), 
+      RawData.class, getEntityName(), id);
+    if (rd == null) throw new ItemNotFoundException("RawData[id = " + id + "]");
+    
+    RawDataUtil.getRawBioAssay(dc, rd); // To check for read permission
+    return rd;
+  }
+  
 }

trunk/src/core/net/sf/basedb/core/query/ExpressionSelect.java

@@ -46 +46 @@
   private final Expression e1;
   private final String alias;
+  private final boolean useInDistinctCount;
 
-  ExpressionSelect(Expression e1, String alias)
+  ExpressionSelect(Expression e1, String alias, boolean useInDistinctCount)
   {
     this.e1 = e1;
     this.alias = alias;
+    this.useInDistinctCount = useInDistinctCount;
   }
 
@@ -80 +82 @@
     return e1;
   }
+  public boolean useInDistinctCount()
+  {
+    return useInDistinctCount;
+  }
   // -------------------------------------------
   /*

trunk/src/core/net/sf/basedb/core/query/Select.java

@@ -55 +55 @@
   */
   public Expression getExpression();
+  
+  /**
+    If this expression should be use in count distinct queries or not.
+    <pre class="code">
+SELECT COUNT(DISTINCT expression)
+</pre>
+    @return TRUE or FALSE
+  */
+  public boolean useInDistinctCount();
 
 }

trunk/src/core/net/sf/basedb/core/query/Selects.java

@@ -45 +45 @@
 
   /**
-    Create a selection from an expression, optionally giving it an alias. 
-    The alias can be used when getting the result to find the column
-    index. See {@link SqlResultIterator#getIndex(String)}.
-    <p>
-<pre class="code">
-SELECT <i>&lt;expression&gt;</i> AS <i>&lt;alias&gt;</i>
-FROM ...
-</pre>
-    <p>
-    TODO - more example code
-    
-    @param e1 The expression to select
-    @param alias The alias to give the expression
-    @return A selection query element
-    @throws InvalidDataException If the expression is null or if the
-      alias contains invalid characters 
+    Same as <code>expression(e1, alias, false)</code>.
+    @see #expression(Expression, String, boolean)
   */
   public static final Select expression(Expression e1, String alias)
@@ -70 +56 @@
       throw new InvalidDataException("Alias '"+alias+"' has one or more invalid characters. Only a-z, A-Z and 0-9 is allowed.");
     }
-    return new ExpressionSelect(e1, alias);
+    return new ExpressionSelect(e1, alias, false);
+  }
+  
+  /**
+    Create a selection from an expression, optionally giving it an alias. 
+    The alias can be used when getting the result to find the column
+    index. See {@link SqlResultIterator#getIndex(String)}.
+    <p>
+  <pre class="code">
+SELECT <i>&lt;expression&gt;</i> AS <i>&lt;alias&gt;</i>
+FROM ...
+  </pre>
+    <p>
+    The useInDistinctCount parameter affects the {@link Query#count(DbControl)}
+    method, if the {@link Query#setDistinct(boolean)} has been set to true. In this
+    case only expressions which has been created for use with the distinct function
+    are used in the selection list:
+    <pre class="code">
+SELECT COUNT(DISTINCT <i>&lt;expression&gt;</i>)
+FROM ...
+  </pre>
+    <p>
+    
+    TODO - more example code
+    
+    @param e1 The expression to select
+    @param alias The alias to give the expression
+    @param useInDistinctCount If the expression should be used when counting distinct values
+    @return A selection query element
+    @throws InvalidDataException If the expression is null or if the
+      alias contains invalid characters 
+  */  
+  public static final Select expression(Expression e1, String alias, boolean useInDistinctCount)
+    throws InvalidDataException
+  {
+    if (e1 == null) throw new InvalidUseOfNullException("e1");
+    if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
+    {
+      throw new InvalidDataException("Alias '"+alias+"' has one or more invalid characters. Only a-z, A-Z and 0-9 is allowed.");
+    }
+    return new ExpressionSelect(e1, alias, useInDistinctCount);
   }
   

trunk/www/include/styles/main.css

@@ -173 +173 @@
 a.disabled {
   color: #666666;
-  xtext-decoration: none;
   cursor: default;
 }
@@ -182 +181 @@
 .form .prompt {
   font-weight: bold;
-  padding: 2px 4px 2px 0px;
+  padding: 2px 4px 2px 2px;
   white-space: nowrap;
-}
+  background: #E0E0E0;
+}
+
+.form tr {
+  vertical-align: top;
+}
+      
 
 .error {

trunk/www/views/experiments/bioassaysets/view_bioassayset.jsp

@@ -232 +232 @@
         image="explorer.png"
         onclick="<%="openExperimentExplorer(" + itemId + ")"%>"
-        title="Experiment explorer&hellip;"
+        title="Experiment explorer"
         tooltip="View the data reporter by reporter"
       />

trunk/www/views/experiments/explorer/search/index.jsp

@@ -41 +41 @@
 <%!
   private static final Item itemType = Item.REPORTER;
-  private static final ItemContext defaultContext = 
-    Base.createDefaultContext("@externalId", "name,externalId");
+
 %>
 <%
@@ -66 +65 @@
   if (cmd == null || "List".equals(cmd))
   {
-    ItemContext cc = explorer.getAndSetReporterContext(sc, null, defaultContext);
+    ItemContext cc = explorer.getAndSetReporterContext(sc, null);
     redirect = listPage;
   }
   else if ("UpdateContext".equals(cmd))
   {
-    ItemContext cc = explorer.getAndSetReporterContext(sc, pageContext, defaultContext);
+    ItemContext cc = explorer.getAndSetReporterContext(sc, pageContext);
     redirect = listPage;
-//    throw new WebException("popup", "Page", request.getParameter("page") + ":" + cc.getPage()+":"+request.getParameter("sortby")+":"+cc.getSortProperty());
   }
   else

trunk/www/views/experiments/explorer/search/list.jsp

@@ -84 +84 @@
   
   final ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bioAssaySet);
-  final ItemContext cc = explorer.getAndSetReporterContext(sc, null, null);
+  final ItemContext cc = explorer.getAndSetReporterContext(sc, null);
   final String subContext = cc.getSubContext();
 
   List<TableColumn> columns = new LinkedList<TableColumn>();
-  //DynamicUtil.addSpotColumns(columns, rawDataType.getChannels());
-  //DynamicUtil.addRawDataColumns(columns, rawDataType, "raw.", "$", "[Raw] ");
   DynamicUtil.addReporterColumns(columns, "", "@", "");
   
@@ -98 +96 @@
     selectedIndex.put(selected.selectedIds.get(i), i+2);  
   }
-  /*
-  final int matchingReporters = explorer.getMatchingReporters();
-  final int reporterIndex = explorer.getReporterIndex();
-  final int positionIndex = explorer.getPositionIndex();
-  final ReporterData reporter = explorer.getReporter(dc, reporterIndex);
-  final int matchingPositions = explorer.getNumPositions(dc, reporter);
-  */
   
   DynamicSpotQuery reporterQuery = explorer.getReporterQuery(dc, selected.selectedProperties);

trunk/www/views/experiments/explorer/view/index.jsp

@@ -62 +62 @@
   BioAssaySet bioAssaySet = BioAssaySet.getById(dc, bioAssaySetId);
   ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bioAssaySet);
-  if (cmd == null)
+  if (cmd == null || "Explore".equals(cmd))
   {
-    explorer.setReporterIndex(0);
-    explorer.setPositionIndex(0);
+    //explorer.setReporterIndex(0);
+    //explorer.setPositionIndex(0);
     redirect = viewPage;
   }
@@ -81 +81 @@
   {
     explorer.setPositionIndex(Values.getInt(request.getParameter("spotIndex")));
+    redirect = viewPage;
+  }
+  else if ("SetAnnotationType".equals(cmd))
+  {
+    explorer.setAnnotationTypeId(Values.getInt(request.getParameter("annotationtype_id")));
+    
+    // Fix visible columns
+    ItemContext cc = explorer.getAndSetSpotContext(sc, null);
+    String columns = cc.getSetting("columns");
+    if (explorer.getAnnotationTypeId() != 0)
+    {
+      if (!columns.contains("annotation")) columns = "annotation," + columns;
+    }
+    else
+    {
+      columns.replace("annotation", "");
+    }
+    cc.setSetting("columns", columns);
     redirect = viewPage;
   }

trunk/www/views/experiments/explorer/view/view.jsp

@@ -30 +30 @@
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.BioAssaySet"
+  import="net.sf.basedb.core.BioAssay"
   import="net.sf.basedb.core.Experiment"
   import="net.sf.basedb.core.RawDataType"
+  import="net.sf.basedb.core.RawBioAssay"
+  import="net.sf.basedb.core.RawDataUtil"
   import="net.sf.basedb.core.ExtendedProperties"
   import="net.sf.basedb.core.ExtendedProperty"
+  import="net.sf.basedb.core.AnnotationType"
+  import="net.sf.basedb.core.Annotation"
+  import="net.sf.basedb.core.Formula"
+  import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.DynamicSpotQuery"
   import="net.sf.basedb.core.DynamicResultIterator"
   import="net.sf.basedb.core.VirtualColumn"
+  import="net.sf.basedb.core.Type"
   import="net.sf.basedb.core.data.ReporterData"
+  import="net.sf.basedb.core.data.RawData"
   import="net.sf.basedb.core.query.Restrictions"
   import="net.sf.basedb.core.query.Expressions"
@@ -55 +66 @@
   import="net.sf.basedb.clients.web.taglib.table.TableColumn"
   import="java.util.Date"
+  import="java.util.Set"
+  import="java.util.HashSet"
   import="java.util.List"
   import="java.util.LinkedList"
@@ -83 +96 @@
   final ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bioAssaySet);
   final ItemContext cc = explorer.getAndSetSpotContext(sc, pageContext);
+  final ItemContext reporterContext = explorer.getAndSetReporterContext(sc, null);
   final String subContext = cc.getSubContext();
-
+  
   List<TableColumn> columns = new LinkedList<TableColumn>();
   DynamicUtil.addSpotColumns(columns, rawDataType.getChannels());
+  DynamicUtil.addFormulaColumns(columns, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, "frm", "");
   DynamicUtil.addRawDataColumns(columns, rawDataType, "raw.", "$", "[Raw] ");
-  //DynamicUtil.addReporterColumns(columns, "rep.", "@", "[Rep] ");
   // TODO - DynamicUtil.addExtraColumns(columns);
-  // TODO - DynamicUtil.addFormulaColumns(columns);
-  
-  columns.remove(0);
+  columns.add(new TableColumn("raw.spotimage", "$id", "raw('id')", Type.INT, "[Raw] Spotimage", "", "auto", false, false, false));
+
+  columns.remove(0); // The position column, it is added in another place
   
   DynamicUtil.SelectedInfo selected = DynamicUtil.getSelectedColumns(cc, columns);
+  
+  final int annotationTypeId = explorer.getAnnotationTypeId();
+  final AnnotationType annotationType = annotationTypeId == 0 ? 
+    null : AnnotationType.getById(dc, annotationTypeId);
   
   final int matchingReporters = explorer.getMatchingReporters(dc);
@@ -145 +163 @@
       Forms.createHidden(frm, 'spotIndex', spotIndex-1);
       return true;
+    }
+    function annotationTypeOnChange()
+    {
+      var frm = document.forms['explorer'];
+      frm.cmd.value = 'SetAnnotationType';
+      frm.submit();
     }
     function viewSearch()
@@ -178 +202 @@
     
     <t:tab id="view" title="Reporter view">
-
     <div class="boxed">
     
@@ -186 +209 @@
     <input type="hidden" name="cmd" value="">
     
-      
+    
+    <table width="100%" cellspacing="2" cellpadding="0" border="0">
+    <tr valign="bottom">
+      <td width="50%">
+
       <h4>Current reporter
       <input name="newReporterIndex" type="text" class="text" value="<%=reporterIndex+1%>" 
@@ -231 +258 @@
       %>
       </h4>
-      <p>
-      
+      
+      </td>
+      <td width="50%">
+        <h4>Annotation</h4>
+      </td>
+      </tr>
+      
+      <tr valign="top">
+      <td>
+
       <%
       if (reporter != null)
       {
         %>
-        <table class="form" cellspacing=0>
+        <table class="form" cellspacing=0 width="100%">
         <tr>
-          <td class="prompt">Name</td>
+          <td class="prompt" >Name</td>
           <td colspan="7"><%=Base.getLink(ID, reporter.getName(), Item.REPORTER, reporter.getId(), true)%></td>
         </tr>
@@ -248 +283 @@
           <td class="prompt">Type</td>
           <td><base:propertyvalue dbcontrol="<%=dc%>" item="<%=reporter%>" property="reporterType" /></td>
-          <td>&nbsp;&nbsp;</td>
+        </tr>
+        <tr valign="top">
           <td class="prompt">Gene symbol</td>
           <td><%=HTML.encodeTags(reporter.getSymbol())%></td>
+          <td>&nbsp;&nbsp;</td>
+          <td class="prompt">Description</td>
+          <td><%=HTML.niceFormat(reporter.getDescription())%></td>
         </tr>
         <tr valign="top">
-          <td class="prompt">Description</td>
-          <td><%=HTML.niceFormat(reporter.getDescription())%></td>
-          <td>&nbsp;&nbsp;</td>
           <td class="prompt">Last update</td>
           <td><%=Values.formatDate(reporter.getLastUpdate())%></td>
           <td>&nbsp;&nbsp;</td>
           <%
-          int column = 2;
+          int column = 1;
           for (ExtendedProperty ep : ExtendedProperties.getProperties("ReporterData"))
           {
@@ -267 +303 @@
             String link = ep.getUrl(value);
             if (value instanceof Date) value = Values.formatDate((Date)value);
-            value = value == null ? "<i>- no value -</i>" : HTML.encodeTags(value.toString());
+            value = value == null ? "" : HTML.encodeTags(value.toString());
             if (link != null)
             {
@@ -277 +313 @@
               <td><%=value%></td>
               <td>&nbsp;&nbsp;</td>
-              <%=column == 2 ? "</tr>" : ""%>
+              <%=column == 1 ? "</tr>" : ""%>
             <%
             column++;
-            if (column > 2) column = 0;
+            if (column > 1) column = 0;
           }
           %>
-          <%=column < 2 ? "</tr>" : ""%>
+          <%=column < 1 ? "</tr>" : ""%>
         </table>
 
@@ -349 +385 @@
         }
         %>
-        <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=-1"
+        [ <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=-1"
           title="Show all positions">all</a>
-        <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=-2"
+        | <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=-2"
           title="Calculate average values for each bioassay">avg</a>
+        ]
         <%
       }
       %>
       </h4>
+      
+      </td>
+      <td>
+        <select name="annotationtype_id" onchange="annotationTypeOnChange()">
+        <option value="0">- none -
+        <%
+        ItemQuery<AnnotationType> annotationTypeQuery = experiment.getExperimentalFactors();
+        annotationTypeQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+        ItemResultIterator<AnnotationType> annotationTypes = annotationTypeQuery.iterate(dc);
+        while (annotationTypes.hasNext())
+        {
+          AnnotationType at = annotationTypes.next();
+          String isSelected = at.getId() == annotationTypeId ? "selected" : "";
+          %>
+          <option value="<%=at.getId()%>" <%=isSelected%>><%=HTML.encodeTags(at.getName())%>
+          <%
+        }
+        %>
+        </select>
+        <p>
+        <%
+        if (annotationType != null)
+        {
+          %>
+          <b>Summary</b><br>
+          TODO
+          <%
+        }
+        %>
+      </td>
+      </tr>
+      </table>
+      
       </form>
       
@@ -375 +445 @@
         value="<%=String.valueOf(bioAssaySetId)%>" 
       />
+      <%
+      if (annotationType != null)
+      {
+        %>
+        <tbl:columndef
+          id="annotation"
+          title="<%=HTML.encodeTags(annotationType.getName()) %>"
+          show="always"
+        />
+        <%
+      }
+      %>
       <tbl:columndef
         id="bioassay"
+        property="COLUMN"
         title="Bioassay"
         show="always"
+        sortable="true"
       />
       <tbl:columndef
         id="position"
+        property="POSITION"
         title="Position"
         show="<%=positionIndex == ExperimentExplorer.SPOT_AVG ? "never" : "always" %>"
+        sortable="true"
       />
       <tbl:columndef
@@ -417 +503 @@
       </tbl:toolbar>
       <tbl:data>
-        <tbl:columns>
-        </tbl:columns>
+        <tbl:columns />
         <tbl:rows>
-        
       <%
       int index = 0;
@@ -430 +514 @@
         %>
         <tbl:row>
+          <%
+          if (annotationType != null)
+          {
+            BioAssay ba = explorer.getBioAssay(dc, item.getShort(1));
+            ItemQuery<RawBioAssay> rbaQuery = ba.getRawBioAssays();
+            rbaQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+            List<RawBioAssay> rba = rbaQuery.list(dc);
+
+            Set<Object> allValues = new HashSet<Object>();
+            for (RawBioAssay rb : rba)
+            {
+              Annotation a = rb.isAnnotated() ? 
+                rb.getAnnotationSet().findAnnotation(annotationType) : null;
+              allValues.addAll(a.getValues());
+            }
+            %>
+            <tbl:cell column="annotation">
+            <%=Values.getString(allValues, ", ", true)%>
+            </tbl:cell>
+            <%
+          }
+          %>
           <tbl:cell column="bioassay"><%=Base.getLinkedName(ID, explorer.getBioAssay(dc, item.getShort(1)), false, true)%></tbl:cell>
           <tbl:cell column="position"><%=item.getInt(2)%></tbl:cell>
@@ -435 +541 @@
           <%
           int i = 3;
+          int spotImageIndex = 0;
           for (String columnId : selected.selectedIds)
           {
-            Object value = item.getObject(i++);
-            %>
-            <tbl:cell column="<%=columnId%>"><%=value%></tbl:cell>
-            <%
+            if ("raw.spotimage".equals(columnId))
+            {
+              RawData rd = rawDataType.getRawDataById(dc, item.getInt(i++));
+              RawBioAssay rba = RawDataUtil.getRawBioAssay(dc, rd);
+              %>
+              <tbl:cell column="raw.spotimage">
+                <%
+                if (rba.hasSpotImages())
+                {
+                  %>
+                  <img src="../../../rawbioassays/rawdata/spotimage/<%=ID%>/<%=rba.getId()%>/<%=rd.getId()%>/spot<%=rd.getPosition()%>.png">
+                  <%
+                }
+                else
+                {
+                  %>
+                  <i>- none -</i>
+                  <%
+                }
+                %>
+              </tbl:cell>
+              <%
+            }
+            else
+            {
+              Object value = item.getObject(i++);
+              %>
+              <tbl:cell column="<%=columnId%>"><%=value%></tbl:cell>
+              <%
+            }
           }
           %>