Changeset 5940

Timestamp:

Jan 31, 2012, 1:29:11 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #1655: GUI improvements

• Transformations
• Extra values
• Bioassays
• Experiment explorer

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Form.java (modified) (5 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Header.java (modified) (5 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Label.java (modified) (8 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Panel.java (modified) (6 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Row.java (modified) (7 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java (modified) (1 diff)
• www/WEB-INF/table.tld (modified) (7 diffs)
• www/exception/exception.jsp (modified) (2 diffs)
• www/include/scripts/exception.js (modified) (1 diff)
• www/include/scripts/main.js (modified) (2 diffs)
• www/include/styles/explorer.css (modified) (1 diff)
• www/include/styles/main.css (modified) (1 diff)
• www/include/styles/table.css (modified) (2 diffs)
• www/include/styles/toolbar.css (modified) (3 diffs)
• www/views/experiments/bioassays/view_bioassay.jsp (modified) (3 diffs)
• www/views/experiments/bioassaysets/view_bioassayset.jsp (modified) (8 diffs)
• www/views/experiments/explorer/view/view.jsp (modified) (13 diffs)
• www/views/experiments/extravalues/view_extravalue.jsp (modified) (9 diffs)
• www/views/experiments/transformations/view_transformation.jsp (modified) (6 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java

@@ -45 +45 @@
 import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.JspTagException;
-import javax.servlet.jsp.tagext.TagSupport;
 
 

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Form.java

@@ -27 +27 @@
 import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.JspTagException;
-import javax.servlet.jsp.tagext.TagSupport;
+
+import net.sf.basedb.clients.web.taglib.StylableTag;
+
 
 
@@ -77 +79 @@
 */
 public class Form
-  extends TagSupport
+  extends StylableTag
 {
 
@@ -85 +87 @@
   
   private int width = 1;
+  
+  public Form()
+  {
+    super(null);
+  }
   
   public void setWidth(int width)
@@ -111 +118 @@
     Map<String, String> contents = table.getColumnContent();
     StringBuilder sb = new StringBuilder();
+    sb.append("<table ");
+    addIdAndStyles(sb);
+    sb.append(">\n");
     int colNum = 0;
     for (String col : table.getVisibleColumns())
     {
       String header = headers.get(col);
-      if (header == null) header = "<td>&nbsp;</td>";
+      if (header == null) header = "<th></th>";
       String content = contents.get(col);
-      if (content == null) content = "<td>&nbsp;</td>";
+      if (content == null) content = "<td></td>";
       if (colNum % width == 0) sb.append("<tr>");
       sb.append(header);
@@ -124 +134 @@
       if (colNum % width == 0) sb.append("</tr>");
     }
-    if (colNum % width != 0) sb.append("</tr>");
+    while (colNum % width != 0)
+    {
+      sb.append("<th></th><td></td>");
+      colNum++;
+      if (colNum % width == 0) sb.append("</tr>");
+    }
     contents.clear();
+    
+    sb.append("</table>");
     try
     {

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Header.java

@@ -26 +26 @@
 import javax.servlet.jsp.JspTagException;
 import javax.servlet.jsp.tagext.Tag;
-import javax.servlet.jsp.tagext.TagSupport;
+
+import net.sf.basedb.clients.web.taglib.StylableTag;
 
 /**
@@ -86 +87 @@
 */
 public class Header
-  extends TagSupport
+  extends StylableTag
 {
 
@@ -94 +95 @@
   private static final long serialVersionUID = -7541520513764712983L;
 
+  public Header()
+  {
+    super(null);
+  }
+  
   /**
     The parent <tbl:table> tag.
   */
   private Table table;
-  
-  /**
-    Optional <code>class</code> attribute
-  */
-  private String clazz = "header";
-  
-  /**
-    Optional <code>style</code> attribute
-  */
-  private String style = null;
-  
+    
   /**
     If the header should be visible or not.
@@ -117 +113 @@
     Taglib initialization methods
   */
-  public void setClazz(String clazz)
-  {
-    this.clazz = clazz;
-  }
-  public String getClazz()
-  {
-    return clazz;
-  }
 
-  public void setStyle(String style)
-  {
-    this.style = style;
-  }
-  public String getStyle()
-  {
-    return style;
-  }
-  
   public void setVisible(boolean visible)
   {
@@ -169 +148 @@
     StringBuilder sb = new StringBuilder();
     sb.append("<th");
-    if (getClazz() != null) sb.append(" class=\"").append(getClazz()).append("\"");
-    if (getStyle() != null) sb.append(" style=\"").append(getStyle()).append("\"");
+    addIdAndStyles(sb);
     sb.append(">");
     try

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Label.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.taglib.Page;
+import net.sf.basedb.clients.web.taglib.StylableTag;
 
 import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.JspTagException;
-import javax.servlet.jsp.tagext.TagSupport;
 
 /**
@@ -131 +131 @@
 */
 public class Label
-  extends TagSupport
+  extends StylableTag
 {
 
@@ -139 +139 @@
   private static final long serialVersionUID = 5326481772609709567L;
 
+  public Label()
+  {
+    super("label");
+  }
+  
+  
   /**
     The parent <tbl:table> tag.
@@ -149 +155 @@
   private Toolbar toolbar;
 
-  /**
-    Optional <code>class</code> attribute
-  */
-  private String clazz = "label";
-  
-  /**
-    Optional <code>style</code> attribute
-  */
-  private String style = null;
-  
   /**
     An optional image to show in the button.
@@ -182 +178 @@
     Taglib initialization methods
   */
-  public void setClazz(String clazz)
-  {
-    this.clazz = clazz;
-  }
-  public String getClazz()
-  {
-    return clazz;
-  }
-
-  public void setStyle(String style)
-  {
-    this.style = style;
-  }
-  public String getStyle()
-  {
-    return style;
-  }
-
   public void setImage(String image)
   {
@@ -252 +230 @@
     StringBuilder sb = new StringBuilder();
     sb.append("<td");
-    if (getId() != null) sb.append(" id=\"").append(getId()).append("\"");
-    if (getClazz() != null)
-    {
-      sb.append(" class=\"").append(getClazz()).append("\"");
-    }
-    if (getStyle() != null) sb.append(" style=\"").append(getStyle()).append("\"");
+    addIdAndStyles(sb);
     String tooltip = getTooltip();
     if (!displayText && tooltip == null) tooltip = getTitle();
@@ -264 +237 @@
     if (displayImage)
     {
-      sb.append("<table border=\"0\" cellspacing=\"0\" cellpadding=\"0\"><tr><td>");
+      sb.append("<table><tr><td>");
       sb.append("<img src=\"").append(page.getRoot()).append("images/").append(getImage()).append("\"");
-      sb.append(" border=\"0\"></td><td>");
-    }
-    if (displayText && getTitle() != null) sb.append("&nbsp;").append(getTitle()).append("&nbsp;");
+      sb.append("></td><td>");
+    }
+    if (displayText && getTitle() != null) 
+    {
+      sb.append("<span style=\"padding: 0px 2px 0px 2px;\"");
+      if (getId() != null) sb.append(" id=\"").append(getId()).append(".text").append("\"");
+      sb.append(">").append(getTitle());
+    }
+    try
+    {
+      pageContext.getOut().print(sb.toString());
+    }
+    catch (Exception ex)
+    {
+      throw new JspTagException(ex.getMessage());
+    }
+    return EVAL_BODY_INCLUDE;
+  }
+
+  public int doEndTag()
+      throws JspException
+  {
+    boolean displayImage = getImage() != null && toolbar.hasImages();
+    boolean displayText = toolbar.hasText() || !displayImage;
+    
+    StringBuilder sb = new StringBuilder();
+    if (displayText && getTitle() != null) 
+    {
+      sb.append("</span>");
+    }
     if (displayImage)
     {
@@ -282 +282 @@
       throw new JspTagException(ex.getMessage());
     }
-    return SKIP_BODY;
+    return EVAL_BODY_INCLUDE;
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Panel.java

@@ -25 +25 @@
 import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.JspTagException;
-import javax.servlet.jsp.tagext.TagSupport;
+
+import net.sf.basedb.clients.web.taglib.StylableTag;
 
 /**
@@ -101 +102 @@
 */
 public class Panel
-  extends TagSupport
+  extends StylableTag
 {
 
@@ -109 +110 @@
   private static final long serialVersionUID = 8435173953529878997L;
 
-  /**
-    Optional <code>class</code> attribute
-  */
-  private String clazz = "panel";
+  public Panel()
+  {
+    super("panel");
+  }
   
-  /**
-    Optional <code>style</code> attribute
-  */
-  private String style = null;
-
   /**
     If the panel should be visible or not.
@@ -127 +123 @@
     Taglib initialization methods
   */
-  public void setClazz(String clazz)
-  {
-    this.clazz = clazz;
-  }
-  public String getClazz()
-  {
-    return clazz;
-  }
-
-  public void setStyle(String style)
-  {
-    this.style = style;
-  }
-  public String getStyle()
-  {
-    return style;
-  }
 
   public void setVisible(boolean visible)
@@ -163 +142 @@
 
     StringBuilder sb = new StringBuilder();
-    sb.append("<tr><td");
-    if (getId() != null) sb.append(" id=\"").append(getId()).append("\"");
-    if (getClazz() != null) sb.append(" class=\"").append(getClazz()).append("\"");
-    if (getStyle() != null) sb.append(" style=\"").append(getStyle()).append("\"");
+    sb.append("<div");
+    addIdAndStyles(sb);
     sb.append(">\n");
     try
@@ -184 +161 @@
     if (!isVisible()) return EVAL_PAGE;
     StringBuilder sb = new StringBuilder();
-    sb.append("</td></tr>\n");
+    sb.append("</div>\n");
     try
     {

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Row.java

@@ -25 +25 @@
 import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.JspTagException;
-import javax.servlet.jsp.tagext.TagSupport;
+
+import net.sf.basedb.clients.web.taglib.StylableTag;
 
 /**
@@ -111 +112 @@
 */
 public class Row
-  extends TagSupport
+  extends StylableTag
 {
 
@@ -119 +120 @@
   private static final long serialVersionUID = 1975591924471893645L;
 
+  public Row()
+  {
+    super(null);
+  }
+  
   /**
     The parent <tbl:table> tag.
@@ -129 +135 @@
   private Data data;
 
-  /**
-    Optional <code>class</code> attribute
-  */
-  private String clazz = null;
-  
-  /**
-    Optional <code>style</code> attribute
-  */
-  private String style = null;
-  
   /**
     Optional <code>class</code> attribute that is applied when the mouse is over the current row.
@@ -152 +148 @@
     Taglib initialization methods
   */
-  public void setClazz(String clazz)
-  {
-    this.clazz = clazz;
-  }
-  public String getClazz()
-  {
-    return clazz;
-  }
-
-  public void setStyle(String style)
-  {
-    this.style = style;
-  }
-  public String getStyle()
-  {
-    return style;
-  }
-
   public void setHightligh(String highlight)
   {
@@ -178 +156 @@
     return highlight;
   }
-  
   
   public void setVisible(boolean visible)
@@ -206 +183 @@
     if (!isVisible()) return SKIP_BODY;
 
-    String clazz = getClazz() == null ? table.getNextRowClass() : getClazz();
-    if (getHighlight() != null) clazz += " " + getHighlight();
     StringBuilder sb = new StringBuilder();
     sb.append("<tr");
-    if (getId() != null) sb.append(" id=\"").append(getId()).append("\"");
-    sb.append(" class=\"").append(clazz).append("\"");
-    if (getStyle() != null) sb.append(" style=\"").append(getStyle()).append("\"");
+    addIdAndStyles(sb, table.getNextRowClass(), getHighlight());
     sb.append(">\n");
-
     try
     {

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java

@@ -43 +43 @@
 import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.JspTagException;
-import javax.servlet.jsp.tagext.TagSupport;
 import javax.servlet.http.HttpServletRequest;
 

trunk/www/WEB-INF/table.tld

@@ -123 +123 @@
     </attribute>
     <attribute>
+      <name>subclass</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>style</name>
       <required>false</required>
@@ -429 +434 @@
     </attribute>
     <attribute>
+      <name>subclass</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>style</name>
       <required>false</required>
@@ -514 +524 @@
     </attribute>
     <attribute>
+      <name>subclass</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>style</name>
       <required>false</required>
@@ -553 +568 @@
     </attribute>
     <attribute>
+      <name>subclass</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>style</name>
       <required>false</required>
@@ -568 +588 @@
     <tagclass>net.sf.basedb.clients.web.taglib.table.Header</tagclass>
     <attribute>
-      <name>clazz</name>
+      <name>id</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>clazz</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>subclass</name>
       <required>false</required>
       <rtexprvalue>true</rtexprvalue>
@@ -603 +633 @@
     </attribute>
     <attribute>
+      <name>subclass</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>style</name>
       <required>false</required>
@@ -732 +767 @@
     <tagclass>net.sf.basedb.clients.web.taglib.table.Form</tagclass>
     <attribute>
+      <name>id</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>clazz</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>subclass</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>style</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>width</name>
       <required>false</required>

trunk/www/exception/exception.jsp

@@ -110 +110 @@
 %>
 <base:page type="default" menu="exception" title="Unexpected error">
-<base:head scripts="exception.js" />
+<base:head scripts="exception.js" styles="popup.css" />
 <base:body onload="Exception.fixWindow(true)">
-  <base:note type="error" title="<%=exceptionClassName + " on page "+request.getAttribute("javax.servlet.error.request_uri")%>" 
-    style="width:90%;" messagestyle="height: 450px;">
-    <table border="0" cellpadding="0" cellspacing="0" class="form">
-    <tr>
-      <td class="prompt">Version</td>
-      <td class="info"><%=Application.getVersionString()%></td>
-    </tr>
-    <tr>
-      <td class="prompt">Web server</td>
-      <td class="info"><%=application.getServerInfo()%></td>
-    </tr>
-    <tr>
-      <td class="prompt">Database Server</td>
-      <td class="info"><%=Application.getDatabaseVersionString()%></td>
-    </tr>
-    <tr>
-      <td class="prompt">Database Dialect</td>
-      <td class="info"><%=Config.getString("db.dialect")%></td>
-    </tr>
-    <tr>
-      <td class="prompt">JDBC Driver</td>
-      <td class="info"><%=jdbcDriver%> <%=driverVersion%></td>
-    </tr>
-    <tr>
-      <td class="prompt">Java runtime</td>
-      <td class="info"><%=properties.getProperty("java.runtime.name")%> 
-        (<%=properties.getProperty("java.runtime.version")%>), 
-        <a href="<%=properties.getProperty("java.vendor.url")%>" target="_new"><%=properties.getProperty("java.vendor")%></a></td>
-    </tr>
-    <tr>
-      <td class="prompt">Operating system</td>
-      <td class="info"><%=properties.getProperty("os.name")%> 
+  <h1><%=exceptionClassName + " on page "+request.getAttribute("javax.servlet.error.request_uri")%></h1>
+  <div class="content bottomborder" style="bottom: 3em;">
+    <table class="fullform outlined topborder">
+    <tr>
+      <th>BASE Version</th>
+      <td><%=Application.getVersionString()%></td>
+    </tr>
+    <tr>
+      <th>Web server</th>
+      <td><%=application.getServerInfo()%></td>
+    </tr>
+    <tr>
+      <th>Database Server</th>
+      <td><%=Application.getDatabaseVersionString()%></td>
+    </tr>
+    <tr>
+      <th>Database Dialect</th>
+      <td><%=Config.getString("db.dialect")%></td>
+    </tr>
+    <tr>
+      <th>JDBC Driver</th>
+      <td><%=jdbcDriver%> <%=driverVersion%></td>
+    </tr>
+    <tr>
+      <th>Operating system</th>
+      <td><%=properties.getProperty("os.name")%> 
         <%=properties.getProperty("os.arch")%>
         <%=properties.getProperty("os.version")%>
@@ -149 +143 @@
     </tr>
     <tr>
-      <td class="prompt">Memory</td>
-      <td class="info">Total: <%=Values.formatBytes(runtime.totalMemory())%><br>
+      <th>Java runtime</th>
+      <td><%=properties.getProperty("java.runtime.name")%> 
+        (<%=properties.getProperty("java.runtime.version")%>), 
+        <a href="<%=properties.getProperty("java.vendor.url")%>" target="_new"><%=properties.getProperty("java.vendor")%></a></td>
+    </tr>
+    <tr>
+      <th class="subprompt">Memory</th>
+      <td>Total: <%=Values.formatBytes(runtime.totalMemory())%><br>
         Free: <%=Values.formatBytes(runtime.freeMemory()) %><br>
         Max: <%=Values.formatBytes(runtime.maxMemory()) %></td>
     </tr>
     <tr>
-      <td class="prompt">Browser</td>
-      <td class="info"><%=HTML.encodeTags(request.getHeader("User-Agent"))%></td>
-    </tr>
-    <tr>
-      <td class="prompt">Error message</td>
-      <td class="info"><%=HTML.formatLineBreaks(HTML.encodeTags(ex.getMessage(), ""))%></td>
-    </tr>
-    <tr>
-      <td class="prompt">Stack trace</td>
-      <td class="info"></td>
-    </tr>
-    </table>
-    
-    <%
-    StackTraceElement[] st = ex.getStackTrace();
-    out.println("<pre>");
-    out.println(exceptionClassName);
-    int i = 0;
-    for (i=0; i < st.length && i < 8; i++)
-    {
-      out.print("...at ");
-      out.println(HTML.encodeTags(st[i].toString().replaceAll("net.sf.basedb.core.", "")));
-    }
-    out.println("</pre>");
-    if ((i < st.length) || (ex.getCause() != null))
-    {
-      out.println("<pre id=\"error_detail\" style=\"display:none;\">");
-      while (ex != null)
-      {
-        for (int j=i; j < st.length; j++)
+      <th>Browser</th>
+      <td><%=HTML.encodeTags(request.getHeader("User-Agent"))%></td>
+    </tr>
+    <tr>
+      <th>Error message</th>
+      <td><%=HTML.formatLineBreaks(HTML.encodeTags(ex.getMessage(), ""))%></td>
+    </tr>
+    <tr class="dynamic">
+      <th>Stacktrace</th>
+      <td>
+        <%
+        StackTraceElement[] st = ex.getStackTrace();
+        out.println("<pre>");
+        out.println(exceptionClassName);
+        int i = 0;
+        for (i=0; i < st.length && i < 8; i++)
         {
           out.print("...at ");
-          out.println(HTML.encodeTags(st[j].toString().replaceAll("net.sf.basedb.core.", "")));
+          out.println(HTML.encodeTags(st[i].toString().replaceAll("net.sf.basedb.core.", "")));
         }
-        ex = ex.getCause();
-        if (ex != null)
+        out.println("</pre>");
+        if ((i < st.length) || (ex.getCause() != null))
         {
-          st = ex.getStackTrace();
-          i = 0;
-          out.print("\nCaused by: "+ex.getClass().getName()+": " + ex.getMessage() + "\n");
+          out.println("<pre id=\"error_detail\" style=\"display:none;\">");
+          while (ex != null)
+          {
+            for (int j=i; j < st.length; j++)
+            {
+              out.print("...at ");
+              out.println(HTML.encodeTags(st[j].toString().replaceAll("net.sf.basedb.core.", "")));
+            }
+            ex = ex.getCause();
+            if (ex != null)
+            {
+              st = ex.getStackTrace();
+              i = 0;
+              out.print("\nCaused by: "+ex.getClass().getName()+": " + ex.getMessage() + "\n");
+            }
+          }
+          out.println("</pre>");
         }
-      }
-      out.println("</pre>");
-    }
-    %>
-    &nbsp;<span id="more_detail">
-      <base:icon image="bullet.gif" clazz="" />
-      <a href="javascript:Main.show('error_detail');Main.hide('more_detail');"><%=st.length-i%> more...</a>
-    </span>
-  </base:note>
-  <base:buttongroup>
+        %>
+        <span id="more_detail">
+          <base:icon image="gonext.png" />
+          <a href="javascript:Main.show('error_detail');Main.hide('more_detail');"><%=st.length-i%> more...</a>
+        </span>
+      
+      </td>
+    </table>
+  </div>
+  
+  <base:buttongroup subclass="dialogbuttons">
     <base:button id="goback" onclick="<%="history.go(-1)"%>" title="Back"/>
     <base:button id="close" onclick="<%="window.top.close()"%>" title="Close"/>

trunk/www/include/scripts/exception.js

@@ -49 +49 @@
       // popup window --> Hide menubar
       Main.hide('menubar');
+      document.body.className = 'popup';
       if (resizeIfPopup)
       {

trunk/www/include/scripts/main.js

@@ -2683 +2683 @@
     var imgRoot = getRoot() + 'images/';
     var text = '<div class="multioptioncontrol">';
-    text += '<table width="100%" border="0" cellspacing="0" cellpadding="0"><tr>';
+    text += '<table><tr>';
     if (multiple)
     {
@@ -2698 +2698 @@
     text += '<td class="link" style="text-align: right;"';
     text += ' title="Perform search" onclick="MultiOptions.activeField.form.submit();">';
-    text += '<img src="' + imgRoot + 'ok.gif"></td>';
+    text += '<img src="' + imgRoot + 'ok.png"></td>';
     text += '</tr></table>';
     text += '</div>';

trunk/www/include/styles/explorer.css

@@ -27 +27 @@
 */
 
-.annotationsummary {
-  border: 1px solid #999999;
+.annotationsummary 
+{
+  border: 1px solid #A0A0A0;
   margin-top: 5px;
 }
 
-.annotationsummary .summaryheader {
+.annotationsummary td 
+{
+  padding: 1px 2px 1px 2px;
+}
+.annotationsummary .summaryheader 
+{
   font-weight: bold;
-  background: #E0E0E0;
-  border-bottom: 1px solid #999999;
+  width: 10em;
+  background: #E8E8E8;
+  border-bottom: 1px solid #A0A0A0;
+}
+.annotationsummary .plotheader 
+{
+  background: #E8E8E8;
+  border-bottom: 1px solid #A0A0A0;
 }
 
-.annotationsummary .groupheader {
+.annotationsummary .groupheader 
+{
   font-weight: bold;
+  width: 10em;
   text-align: right;
-  border-bottom: 1px solid #999999;
-  border-left: 1px solid #999999;
+  border-bottom: 1px solid #A0A0A0;
+  border-left: 1px solid #A0A0A0;
 }
 
-.annotationsummary .value {
+.annotationsummary .value 
+{
   text-align: right;
-  border-left: 1px solid #999999;
+  border-left: 1px solid #A0A0A0;
 }
 

trunk/www/include/styles/main.css

@@ -972 +972 @@
 }
 
+.multioptioncontrol table
+{
+  width: 100%;
+}
+
 .multioptionoptions {
   height: 200px;

trunk/www/include/styles/table.css

@@ -38 +38 @@
 }
 
+/* A panel is a full-width area above the table */
+.itemlist div.panel
+{
+  width: 100%;
+  padding: 1px 4px 2px 6px;
+  height: 1.6em;
+  max-height: 1.75em;
+}
+
 /* The actual table containing data */
 .itemlist table.data
@@ -120 +129 @@
 
 /*
-.itemlist .panel {
-  xborder-top: 1px solid #FFFFFF;
-  xborder-left: 1px solid #FFFFFF;
-  xborder-right: 1px solid #999999;
-  border-bottom: 1px solid #A0A0A0;
-  padding: 3px;
-}
 
 .itemlist .currentpage {

trunk/www/include/styles/toolbar.css

@@ -48 +48 @@
 }
 
-.toolbar .button 
+.toolbar .button
 {
-  padding: 3px;
+  padding: 2px;
   cursor: pointer; 
   white-space: nowrap;
@@ -58 +58 @@
 {
   border: 2px solid #2288AA;
-  padding: 1px;
+  padding: 0px;
   border-radius: 4px;
 }
@@ -78 +78 @@
 }
 
-.toolbar .label {
+.toolbar .label 
+{
   font-weight: bold;
-  border-top: 1px solid #FFFFFF;
-  border-left: 1px solid #FFFFFF;
-  border-bottom: 0px solid #999999;
-  border-right: 2px solid #999999;
-  padding: 3px;
+  padding: 2px;
+  white-space: nowrap;
 }
 

trunk/www/views/experiments/bioassays/view_bioassay.jsp

@@ -124 +124 @@
   </base:head>
   <base:body>
-    <p>
-    <p:path>
-      <p:pathelement title="Experiments" href="<%="../index.jsp?ID="+ID%>" />
-      <p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
-        href="<%="../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experiment.getId()%>" />
-      <p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" 
-        href="<%="index.jsp?ID="+ID+"&bioassayset_id="+bioAssaySet.getId()%>" />
-      <p:pathelement title="<%=HTML.encodeTags(bioAssay.getName())%>" />
-    </p:path>
-
-    <t:tabcontrol id="main" active="<%=tabId%>" switch="switchTab">
+    <p:path><p:pathelement 
+      title="Experiments" href="<%="../index.jsp?ID="+ID%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
+        href="<%="../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experiment.getId()%>"
+      /><p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" 
+        href="<%="index.jsp?ID="+ID+"&bioassayset_id="+bioAssaySet.getId()%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(bioAssay.getName())%>"
+      /></p:path>
+
+    <t:tabcontrol 
+      id="main" 
+      subclass="content mastertabcontrol"
+      active="<%=tabId%>" switch="switchTab">
     <t:tab id="properties" title="Properties">
-    <tbl:toolbar
-      >
-      <tbl:button 
-        disabled="<%=writePermission ? false : true%>" 
-        image="edit.gif" 
-        onclick="editItem()" 
-        title="Edit&hellip;" 
-        tooltip="<%=writePermission ? "Edit this bioassay" : "You do not have permission to edit this bioassay"%>" 
-      />
-      <tbl:button 
-        image="import.gif" 
-        onclick="runPlugin('ImportItem')" 
-        title="Import&hellip;" 
-        tooltip="Import data" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
-      />
-      <tbl:button 
-        image="export.gif" 
-        onclick="runPlugin('ExportItem')" 
-        title="Export&hellip;" 
-        tooltip="Export data" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
-      />
-      <tbl:button 
-        image="runplugin.gif" 
-        onclick="runPlugin('RunPlugin')" 
-        title="Run plugin&hellip;" 
-        tooltip="Run a plugin" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
-      />
-      <tbl:button
-        image="plotter.gif"
-        onclick="openPlotTool()"
-        title="Plot tool&hellip;"
-        tooltip="A simple tool for generating plots"
-        visible="<%=hasDbSpots%>"
-      />
-      <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
-        wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
-      <tbl:button
-        image="help.png"
-        onclick="<%="Main.openHelp('" + ID +"', 'bioassay.view.properties')"%>"
-        title="Help&hellip;"
-        tooltip="Get help about this page"
-      />
-      </tbl:toolbar>
-      
-    <div class="boxedbottom">
-      <div class="itemstatus">Permissions on this item: <i><%=PermissionUtil.getFullPermissionNames(bioAssay)%></i></div>
-      <table class="form" cellspacing=0>
+      <div>
+      <table class="fullform bottomborder">
       <tr>
-        <td class="prompt">Name</td>
+        <th class="itemstatus">
+        </th>
+        <td style="padding: 0px;">
+          <tbl:toolbar subclass="bottomborder">
+            <tbl:button 
+              disabled="<%=writePermission ? false : true%>" 
+              image="edit.gif" 
+              onclick="editItem()" 
+              title="Edit&hellip;" 
+              tooltip="<%=writePermission ? "Edit this bioassay" : "You do not have permission to edit this bioassay"%>" 
+            />
+            <tbl:button 
+              image="import.gif" 
+              onclick="runPlugin('ImportItem')" 
+              title="Import&hellip;" 
+              tooltip="Import data" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
+            />
+            <tbl:button 
+              image="export.gif" 
+              onclick="runPlugin('ExportItem')" 
+              title="Export&hellip;" 
+              tooltip="Export data" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
+            />
+            <tbl:button 
+              image="runplugin.gif" 
+              onclick="runPlugin('RunPlugin')" 
+              title="Run plugin&hellip;" 
+              tooltip="Run a plugin" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
+            />
+            <tbl:button
+              image="plotter.gif"
+              onclick="openPlotTool()"
+              title="Plot tool&hellip;"
+              tooltip="A simple tool for generating plots"
+              visible="<%=hasDbSpots%>"
+            />
+            <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
+              wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
+            <tbl:button
+              image="help.png"
+              onclick="<%="Main.openHelp('" + ID +"', 'bioassay.view.properties')"%>"
+              title="Help&hellip;"
+              tooltip="Get help about this page"
+            />
+          </tbl:toolbar>
+        </td>
+      </tr>
+      <tr>
+        <th>Name</th>
         <td><%=HTML.encodeTags(bioAssay.getName())%></td>
       </tr>
       <tr>
-        <td class="prompt">Spots</td>
+        <th>Spots</th>
         <td>db: <%=bioAssay.getNumSpots()%>; file: <%=bioAssay.getNumFileSpots()%></td>
       </tr>
       <tr >
-        <td class="prompt">Description</td>
+        <th>Description</th>
         <td><%=HTML.encodeTags(bioAssay.getDescription())%></td>
       </tr>
       </table>
+      </div>
 
       <jsp:include page="../../../common/datafiles/list_files.jsp">
@@ -211 +217 @@
       rawQuery.order(Orders.asc(Hql.property("name")));
       ItemResultList<RawBioAssay> rawBioAssays = rawQuery.list(dc);
-      if (rawBioAssays.size() == 0)
-      {
-        %>
-        <h4>Raw bioassays</h4>
-        No raw bioassays are linked to this bioassay
-        (or, you don't have permission to view them).
+      %>
+      <base:section
+        id="rawBioAssaySection"
+        title="<%="Raw bioassays (" + rawBioAssays.size() + ")"%>"
+        context="<%=cc%>"
+        >
         <%
-      }
-      else
-      {
-        %>
-        <base:section
-          id="rawBioAssaySection"
-          title="<%="Raw bioassays (" + rawBioAssays.size() + ")"%>"
-          context="<%=cc%>"
-          >
+        if (rawBioAssays.size() == 0)
+        {
+          %>
+          <div class="messagecontainer note">
+          No raw bioassays are linked to this bioassay
+          (or, you don't have permission to view them).
+          </div>
+          <%
+        }
+        else
+        {
+          %>
           <tbl:table
             id="rawBioAssays"
-            
             columns="all"
             >
-          <tbl:columndef 
-            id="name"
-            title="Name"
-          />
-          <tbl:columndef
-            id="spots"
-            title="Spots"
-          />
-          <tbl:columndef 
-            id="description"
-            title="Description"
-          />
-          <%
-          ItemQuery<AnnotationType> efQuery = experiment.getExperimentalFactors();
-          efQuery.include(Include.ALL);
-          efQuery.order(Orders.asc(Hql.property("name")));
-          ItemResultList<AnnotationType> experimentalFactors = efQuery.list(dc);
-          for (AnnotationType at : experimentalFactors)
-          {
-            Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
+            <tbl:columndef 
+              id="name"
+              title="Name"
+            />
+            <tbl:columndef
+              id="spots"
+              title="Spots"
+            />
+            <tbl:columndef 
+              id="description"
+              title="Description"
+            />
+            <%
+            ItemQuery<AnnotationType> efQuery = experiment.getExperimentalFactors();
+            efQuery.include(Include.ALL);
+            efQuery.order(Orders.asc(Hql.property("name")));
+            ItemResultList<AnnotationType> experimentalFactors = efQuery.list(dc);
+            for (AnnotationType at : experimentalFactors)
+            {
+              Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
+              %>
+              <tbl:columndef
+                id="<%="at"+at.getId()%>"
+                title="<%=HTML.encodeTags(at.getName())%>"
+                formatter="<%=formatter%>"
+              />
+              <%
+            }
             %>
-            <tbl:columndef
-              id="<%="at"+at.getId()%>"
-              title="<%=HTML.encodeTags(at.getName())%>"
-              formatter="<%=formatter%>"
-            />
-            <%
-          }
-          %>
-          <tbl:data>
-            <tbl:columns>
-            </tbl:columns>
-            <tbl:rows>
-            <%
-            for (RawBioAssay item : rawBioAssays)
-            {
-              %>
-              <tbl:row>
-                <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
-                <tbl:cell column="spots"><%=item.getSpots()%></tbl:cell>
-                <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
-                <%
-                AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
-                for (AnnotationType at : experimentalFactors)
-                {
-                  String value = "<i>- none -</i>";
-                  List<Annotation> all = as == null ? null : as.findAnnotations(dc, at, true);
-                  Map<Annotatable, List> factorValues = new HashMap<Annotatable, List>();
-                  if (all != null && all.size() > 0)
+            <tbl:data>
+              <tbl:headers>
+                <tbl:headerrow>
+                  <tbl:columnheaders />
+                </tbl:headerrow>
+              </tbl:headers>
+              <tbl:rows>
+              <%
+              for (RawBioAssay item : rawBioAssays)
+              {
+                %>
+                <tbl:row>
+                  <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
+                  <tbl:cell column="spots"><%=item.getSpots()%></tbl:cell>
+                  <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
+                  <%
+                  AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
+                  for (AnnotationType at : experimentalFactors)
                   {
-                    for (Annotation a : all)
+                    String value = "<i>- none -</i>";
+                    List<Annotation> all = as == null ? null : as.findAnnotations(dc, at, true);
+                    Map<Annotatable, List> factorValues = new HashMap<Annotatable, List>();
+                    if (all != null && all.size() > 0)
                     {
-                      List values = a.getValues();
-                      Annotatable aItem = null;
-                      try
+                      for (Annotation a : all)
                       {
-                        aItem = a.getAnnotationSet().getItem();
-                      }
-                      catch (Throwable t)
-                      {}
-                      List toAdd = factorValues.get(aItem);
-                      if (toAdd == null)
-                      {
-                        toAdd = new LinkedList();
-                        factorValues.put(aItem, toAdd);
-                      }
-                      toAdd.addAll(values);
-                    }
-                  }
-                  %>
-                  <tbl:cell column="<%="at"+at.getId()%>"
-                    >
-                    <%
-                    for (Map.Entry<Annotatable, List> entry : factorValues.entrySet())
-                    {
-                      Annotatable aItem = entry.getKey();
-                      List values = entry.getValue();
-                      %>
-                      <tbl:cellvalue list="<%=values%>" />
-                      <%
-                      if (aItem != null && aItem.hasPermission(Permission.WRITE))
-                      {
-                        %>: <base:icon image="edit.gif" 
-                          onclick="<%="editInheritedAnnotation('"+aItem.getType().name()+"',"+aItem.getId()+","+at.getId()+")"%>" 
-                          tooltip="Modify the values of this experimental factor" />
-                        <%
+                        List values = a.getValues();
+                        Annotatable aItem = null;
+                        try
+                        {
+                          aItem = a.getAnnotationSet().getItem();
+                        }
+                        catch (Throwable t)
+                        {}
+                        List toAdd = factorValues.get(aItem);
+                        if (toAdd == null)
+                        {
+                          toAdd = new LinkedList();
+                          factorValues.put(aItem, toAdd);
+                        }
+                        toAdd.addAll(values);
                       }
                     }
                     %>
-                  </tbl:cell>
-                  <%
-                }
-                %>
-              </tbl:row>
-              <%
-            }
-            %>
-            </tbl:rows>
-          </tbl:data>
+                    <tbl:cell column="<%="at"+at.getId()%>"
+                      >
+                      <%
+                      for (Map.Entry<Annotatable, List> entry : factorValues.entrySet())
+                      {
+                        Annotatable aItem = entry.getKey();
+                        List values = entry.getValue();
+                        %>
+                        <tbl:cellvalue list="<%=values%>" />
+                        <%
+                        if (aItem != null && aItem.hasPermission(Permission.WRITE))
+                        {
+                          %>: <base:icon image="edit.gif" 
+                            onclick="<%="editInheritedAnnotation('"+aItem.getType().name()+"',"+aItem.getId()+","+at.getId()+")"%>" 
+                            tooltip="Modify the values of this experimental factor" />
+                          <%
+                        }
+                      }
+                      %>
+                    </tbl:cell>
+                    <%
+                  }
+                  %>
+                </tbl:row>
+                <%
+              }
+              %>
+              </tbl:rows>
+            </tbl:data>
           </tbl:table>
-        </base:section>
-        <%
-      }
-      %>
+          <%
+        }
+        %>
+      </base:section>
       <jsp:include page="../../../common/anytoany/list_anytoany.jsp">
         <jsp:param name="ID" value="<%=ID%>" />
@@ -342 +353 @@
         <jsp:param name="title" value="Other items related to this bioassay" />
       </jsp:include>
-    </div>
     </t:tab>
     
     <t:tab id="annotations" title="Annotations" 
-      tooltip="View annotation values" class="white">
+      tooltip="View annotation values" clazz="white">
       <jsp:include page="../../../common/annotations/list_annotations.jsp">
         <jsp:param name="item_type" value="<%=itemType.name()%>" />

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

@@ -282 +282 @@
           />
         </th>
-        <td style="padding: 0px;" colspan="2">
+        <td style="padding: 0px;">
           <tbl:toolbar subclass="bottomborder">
             <tbl:button 
@@ -373 +373 @@
       </tr>
     </table>
-    <table style="width: 100%; height: 16em;" class="bottomborder">
+    <table style="width: 100%; height: 22em;" class="bottomborder">
     <tr valign="top">
       <td style="width: 50%; height: 100%;">
@@ -406 +406 @@
         <td><%=HTML.niceFormat(bioAssaySet.getDescription())%></td>
       </tr>
-      <tbody class="sectionheader">
-        <tr>
-          <th colspan="2">Transformation &amp; job</th>
-        </tr>
-      </tbody>
       <tr>
         <th>Transformation</th>
@@ -421 +416 @@
       </tr>
       <tr >
-        <th>Started</th>
+        <th class="subprompt">- started</th>
         <td>
           <%=job == null ? "" : dateTimeFormatter.format(job.getStarted())%>
@@ -427 +422 @@
       </tr>
       <tr>
-        <th>Ended</th>
+        <th class="subprompt">- ended</th>
         <td>
           <%=job == null ? "" : dateTimeFormatter.format(job.getEnded())%>
@@ -433 +428 @@
       </tr>
       <tr>
-        <th>Server</th>
+        <th class="subprompt">- server</th>
         <td>
           <%=job == null ? "" : HTML.encodeTags(job.getServer())%>
         </td>
       </tr>
-      <tr>
-        <th>Description</th>
+      <tr class="dynamic">
+        <th class="subprompt">- description</th>
         <td><%=HTML.niceFormat(transformation.getDescription())%></td>
       </tr>
       </table>
     </td>
-    <td style="width: 50%;" class="leftborder">
+    <td style="width: 50%; height: 100%;" class="leftborder">
       <table class="fullform" >
-      <tbody class="sectionheader">
-        <tr>
-          <th colspan="2">Plugin &amp; parameters</th>
-        </tr>
-      </tbody>
       <tr>
         <th>Plugin</th>
@@ -461 +451 @@
           configuration != null && configuration.hasPermission(Permission.WRITE))%></td>
       </tr>
+      <tbody class="sectionheader">
+        <tr>
+          <th colspan="2">Plugin parameters</th>
+        </tr>
+      </tbody>
         <%
         if (job != null)
@@ -519 +514 @@
             %>
             <tr>
-            <th><span title="<%=description%>"><%=name%></span></th>
+            <th class="subprompt"><span title="<%=description%>">- <%=name%></span></th>
               <td>
                 <%=displayValue%>

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

@@ -88 +88 @@
 <%!
   private static final Item itemType = Item.SPOTDATA;
-  private static final String defaultReporterColumns = "externalId,symbol";
+  private static final String defaultReporterColumns = "filter,externalId,symbol";
 %>
 <%
@@ -101 +101 @@
 try
 {
-  Formatter<Date> dateFormatter = FormatterFactory.getDateTimeFormatter(sc);
+  Formatter<Date> dateTimeFormatter = FormatterFactory.getDateTimeFormatter(sc);
+  Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
   String title = null;
   final BioAssaySet bioAssaySet = BioAssaySet.getById(dc, bioAssaySetId);
@@ -276 +277 @@
     }
   </script>
+  <style>
+    .special td.cell:first-of-type
+    {
+      border-right: 1px solid #A0A0A0;
+    }
+  </style>
   </base:head>
   <base:body>
-    <p>
-    <p:path>
-      <p:pathelement title="Experiments" href="<%="../../index.jsp?ID="+ID%>" />
-      <p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
-        href="<%="../../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experiment.getId()%>" />
-      <p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" 
-        href="<%="../../bioassaysets/index.jsp?ID="+ID+"&cmd=ViewItem&item_id="+bioAssaySetId%>" />
-      <p:pathelement title="Explorer" />
-    </p:path>
+    <p:path><p:pathelement title="Experiments" href="<%="../../index.jsp?ID="+ID%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
+        href="<%="../../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experiment.getId()%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" 
+        href="<%="../../bioassaysets/index.jsp?ID="+ID+"&cmd=ViewItem&item_id="+bioAssaySetId%>" 
+      /><p:pathelement title="Explorer" /></p:path>
     
-    <t:tabcontrol id="explorer" switch="switchTab" remember="false" active="view">
+    <t:tabcontrol
+      id="explorer" 
+      subclass="content mastertabcontrol"
+      switch="switchTab" 
+      remember="false" active="view">
     <t:tab id="search" title="Reporter search" />
     
     <t:tab id="view" title="Reporter view">
-    <div class="boxed">
-    
     <%
     Collection<PropertyFilter> filters = reporterContext.getPropertyFilters();
     String filter = filters != null && filters.size() > 0 ? 
-      "(" + Values.getString(filters, ") AND (", true).replaceAll("@|�", "") + ")" : "- none -";
-    %>
-    <table class="form">
-    <tr>
-      <td class="prompt">Filter</td>
-      <td>
-      <%=HTML.encodeTags(filter)%>
-      </td>
-    </tr>
-    </table>
-    
-    
-    <%
-    if (reporter != null)
+      Values.getString(filters, " AND ", true).replaceAll("@|�", "") : "- none -";
+    if (reporter == null)
+    {
+      %>
+      <table class="fullform bottomborder">
+      <tr>
+        <th>Filter</th>
+        <td><%=HTML.encodeTags(filter)%></td>
+      </tr>
+      <tr>
+        <th class="subprompt"></th>
+        <td>
+          <div class="messagecontainer note">
+          No reporters found.
+          </div>
+        </td>
+      </table>
+      <%
+    }
+    else
     {
       %>
@@ -317 +329 @@
       <input type="hidden" name="bioassayset_id" value="<%=bioAssaySetId%>">
       <input type="hidden" name="cmd" value="SetReporterIndex">
-      <h4 class="docked">Current reporter
+      
+      <tbl:toolbar subclass="bottomborder">
+        <tbl:label style="padding: 0px 2px 0px 6px;">
+          Current reporter
             <input name="newReporterIndex" type="text" class="text" value="<%=reporterIndex+1%>" 
-        onkeypress="return Numbers.integerOnly(event, true, validateReporterIndex)"
-        size="6" maxlength="8" title="Enter a number between 1 and <%=matchingReporters%>">
-      of <%=matchingReporters %>
-      <%
-      if (reporterIndex == 0 || matchingReporters == 0)
-      {
-        %>
-        <base:icon image="first_gray.gif" />
-        <base:icon image="previous_gray.gif" />
-        <%
-      }
-      else
-      {
-        %>
-        <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=0"
-          title="Go the first reporter"><base:icon image="first.gif" /></a>
-        <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=<%=reporterIndex-1%>"
-          title="Go the previous reporter"><base:icon image="previous.gif" /></a>
-        <%
-      }
-      %>
-      &nbsp;&nbsp;
-      <%
-      if (reporterIndex == matchingReporters - 1 || matchingReporters == 0)
-      {
-        %>
-        <base:icon image="next_gray.gif" />
-        <base:icon image="last_gray.gif" />
-        <%
-      }
-      else
-      {
-        %>
-        <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=<%=reporterIndex+1%>"
-          title="Go the next reporter"><base:icon image="next.gif" /></a>
-        <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=<%=matchingReporters-1%>"
-          title="Go the last reporter"><base:icon image="last.gif" /></a>
-        <%
-      }
-      %>
-      </h4>
-      </form>
-      
-      <tbl:toolbar>
+            onkeypress="return Numbers.integerOnly(event, true, validateReporterIndex)"
+            size="6" maxlength="8" title="Enter a number between 1 and <%=matchingReporters%>">
+          of <%=matchingReporters %>
+          <%
+          if (reporterIndex == 0 || matchingReporters == 0)
+          {
+            %>
+            <base:icon image="first_gray.gif" />
+            <base:icon image="previous_gray.gif" />
+            <%
+          }
+          else
+          {
+            %>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=0"
+              title="Go the first reporter"><base:icon image="first.gif" /></a>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=<%=reporterIndex-1%>"
+              title="Go the previous reporter"><base:icon image="previous.gif" /></a>
+            <%
+          }
+          %>
+          &nbsp;&nbsp;
+          <%
+          if (reporterIndex == matchingReporters - 1 || matchingReporters == 0)
+          {
+            %>
+            <base:icon image="next_gray.gif" />
+            <base:icon image="last_gray.gif" />
+            <%
+          }
+          else
+          {
+            %>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=<%=reporterIndex+1%>"
+              title="Go the next reporter"><base:icon image="next.gif" /></a>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetReporterIndex&bioassayset_id=<%=bioAssaySetId%>&reporterIndex=<%=matchingReporters-1%>"
+              title="Go the last reporter"><base:icon image="last.gif" /></a>
+            <%
+          }
+          %>
+        </tbl:label>
         <tbl:button 
           image="columns.gif" 
@@ -370 +382 @@
         />
       </tbl:toolbar>
+      </form>
     
-    <div class="boxedbottom">
-    <tbl:table 
-      id="reporter" 
-      clazz="form" 
-      columns="<%=Values.getString(cc.getSetting("reporter-columns"), defaultReporterColumns)%>"
-      action="index.jsp"
-      sc="<%=sc%>"
-      item="<%=itemType%>"
-      subcontext="<%=subContext%>"
-      >
-      <tbl:hidden 
-        name="bioassayset_id" 
-        value="<%=String.valueOf(bioAssaySetId)%>" 
-      />
-      <%
-      for (TableColumn tc : reporterColumns)
-      {
-        %>
-        <tbl:columndef
-          id="<%=tc.getId()%>"
-          clazz="prompt"
-          title="<%=HTML.encodeTags(tc.getTitle())%>"
-          formatter="<%=tc.getFormatter()%>"
+      <tbl:table 
+        id="reporter" 
+        columns="<%="filter,"+Values.getString(cc.getSetting("reporter-columns"), defaultReporterColumns)%>"
+        action="index.jsp"
+        sc="<%=sc%>"
+        item="<%=itemType%>"
+        subcontext="<%=subContext%>"
+        subclass="bottomborder"
+        >
+        <tbl:hidden 
+          name="bioassayset_id" 
+          value="<%=String.valueOf(bioAssaySetId)%>" 
+        />
+        <tbl:columndef 
+          id="filter" 
+          title="Filter"
+          show="always"
+          subclass="leftborder"
         />
         <%
-      }
-      List<ExtendedProperty> reporterProperties = ExtendedProperties.getProperties("ReporterData");
-      %>
-      <tbl:form width="2">
-        <tbl:cell column="id"><%=reporter.getId()%></tbl:cell>
-        <tbl:cell column="version"><%=reporter.getVersion()%></tbl:cell>
-        <tbl:cell column="name"><%=Base.getLink(ID, reporter.getName(), Item.REPORTER, reporter.getId(), true)%></tbl:cell>
-        <tbl:cell column="externalId"><%=Base.getLink(ID, reporter.getExternalId(), Item.REPORTER, reporter.getId(), true)%></tbl:cell>
-        <tbl:cell column="symbol"><%=HTML.encodeTags(reporter.getSymbol())%></tbl:cell>
-        <tbl:cell column="lastUpdate"><%=dateFormatter.format(reporter.getLastUpdate())%></tbl:cell>
-        <tbl:cell column="type"><base:propertyvalue dbcontrol="<%=dc%>" item="<%=reporter%>" property="reporterType" /></tbl:cell>
-        <tbl:cell column="description"><%=HTML.niceFormat(reporter.getDescription())%></tbl:cell>
-        <%
-        if (reporterProperties != null)
+        for (TableColumn tc : reporterColumns)
         {
-          for (ExtendedProperty ep : reporterProperties)
-          {
-            String name = ep.getName();
-            %>
-            <tbl:cell column="<%=ep.getName()%>"><tbl:cellvalue value="<%=reporter.getExtended(name)%>" /></tbl:cell>
-            <%
-          }
+          %>
+          <tbl:columndef
+            id="<%=tc.getId()%>"
+            title="<%=HTML.encodeTags(tc.getTitle())%>"
+            formatter="<%=tc.getFormatter()%>"
+            show="<%=reporter == null ? "never" : "auto" %>"
+          />
+          <%
         }
+        List<ExtendedProperty> reporterProperties = ExtendedProperties.getProperties("ReporterData");
         %>
-      </tbl:form>
-    </tbl:table>
-    </div>
-    <%
-    }
-    else
-    {
-      %>
-      No reporters found.
-      <%
-    }
-    %>
-    
+        <tbl:form width="2" clazz="fullform special">
+          <tbl:cell column="filter"><%=HTML.encodeTags(filter)%></tbl:cell>
+          <tbl:cell column="id"><%=reporter.getId()%></tbl:cell>
+          <tbl:cell column="version"><%=reporter.getVersion()%></tbl:cell>
+          <tbl:cell column="name"><%=Base.getLink(ID, reporter.getName(), Item.REPORTER, reporter.getId(), true)%></tbl:cell>
+          <tbl:cell column="externalId"><%=Base.getLink(ID, reporter.getExternalId(), Item.REPORTER, reporter.getId(), true)%></tbl:cell>
+          <tbl:cell column="symbol"><%=HTML.encodeTags(reporter.getSymbol())%></tbl:cell>
+          <tbl:cell column="lastUpdate"><%=dateTimeFormatter.format(reporter.getLastUpdate())%></tbl:cell>
+          <tbl:cell column="lastSource"><%=HTML.encodeTags(reporter.getLastSource())%></tbl:cell>
+          <tbl:cell column="entryDate"><%=dateFormatter.format(reporter.getEntryDate()) %></tbl:cell>
+          <tbl:cell column="type"><base:propertyvalue dbcontrol="<%=dc%>" item="<%=reporter%>" property="reporterType" /></tbl:cell>
+          <tbl:cell column="description"><%=HTML.niceFormat(reporter.getDescription())%></tbl:cell>
+          <%
+          if (reporterProperties != null)
+          {
+            for (ExtendedProperty ep : reporterProperties)
+            {
+              String name = ep.getName();
+              %>
+              <tbl:cell column="<%=ep.getName()%>"><tbl:cellvalue value="<%=reporter.getExtended(name)%>" /></tbl:cell>
+              <%
+            }
+          }
+          %>
+        </tbl:form>
+      </tbl:table>
+  
     <base:section
       id="annotation"
       title="<%="Annotation summary (" + selectedAnnotationTypes.size() + " selected)"%>"
       context="<%=cc%>"
+      style="border-bottom: 0px;"
       >
       <form name="annotationSummary" action="index.jsp" method="POST" onsubmit="return false;">
@@ -450 +462 @@
           <input type="hidden" name="annotationtype_id" value="">
           </td></tr></table>
-        <%
-        if (selectedAnnotationTypes.size() > 0)
-        {
+          <%
           for (Map.Entry<AnnotationType, AnnotationSummary> entry : selectedAnnotationTypes.entrySet())
           {
@@ -458 +468 @@
             AnnotationSummary summary = entry.getValue();
             %>
-            <table border="0" cellspacing="0" cellpadding="2" class="annotationsummary">
+            <table class="annotationsummary">
             <tr>
               <td class="summaryheader"><%=Base.getLinkedName(ID, at, false, true)%></td>
-              <td class="summaryheader"><base:icon
+              <td class="plotheader"><base:icon
                 image="plotter.gif"
                 onclick="<%="annotationPlot(" + at.getId() + ")"%>"
@@ -470 +480 @@
               {
                 %>
-                <td class="groupheader" style="background: <%=ag.getColor()%>;" width="50px">
+                <td class="groupheader" style="background: <%=ag.getColor()%>;">
                 <%=ag.getTitle()%>
                 </td>
@@ -538 +548 @@
               </tr>
             </table>
-            <%
-          }
-        }
+          <%
+          }
         %>
-        </form>
+      </form>
     </base:section>
 
-    <form name="spotIndex" action="index.jsp" method="post">
-    <input type="hidden" name="ID" value="<%=ID%>">
-    <input type="hidden" name="bioassayset_id" value="<%=bioAssaySetId%>">
-    <input type="hidden" name="cmd" value="SetSpotIndex">
-    
-      <h4 class="docked">Current spot
-      <input name="newSpotIndex" type="text" class="text" value="<%=positionIndex == -1 ? "all" : positionIndex == -2 ? "avg" : String.valueOf(positionIndex+1)%>" 
-        onkeypress="return Numbers.integerOnly(event, true, validateSpotIndex)"
-        size="6" maxlength="8" title="Enter a number between 1 and <%=matchingPositions%>">
-        of <%=matchingPositions%>
-      
-        <%
-        if (positionIndex == 0)
-        {
-          %>
-          <base:icon image="first_gray.gif" />
-          <%
-        }
-        else
-        {
-          %>
-          <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=0"
-            title="Go the first position"><base:icon image="first.gif" /></a>
-          <%
-        }
-        if (positionIndex <= 0)
-        {
-          %>
-          <base:icon image="previous_gray.gif" />
-          <%
-        }
-        else
-        {
-          %>
-          <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=<%=positionIndex-1%>"
-            title="Go the previous position"><base:icon image="previous.gif" /></a>
-          <%
-        }
-        %>
-        &nbsp;&nbsp;
-        <%
-        if (positionIndex == matchingPositions - 1 || positionIndex < 0)
-        {
-          %>
-          <base:icon image="next_gray.gif" />
-          <%
-        }
-        else
-        {
-          %>
-          <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=<%=positionIndex+1%>"
-            title="Go the next position"><base:icon image="next.gif" /></a>
-          <%
-        }
-        if (positionIndex == matchingPositions - 1)
-        {
-          %>
-          <base:icon image="last_gray.gif" />
-          <%
-        }
-        else
-        {
-          %>
-          <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=<%=matchingPositions-1%>"
-            title="Go the last position"><base:icon image="last.gif" /></a>
-          <%
-        }
-        %>
-        [ <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"
-          title="Calculate average values for each bioassay">avg</a>
-        ]
-        </h4>
-      
-      </form>
     <%
     if (cc.getMessage() != null)
     {
       %>
-      <div class="error"><%=cc.getMessage()%></div>
+      <div class="messagecontainer error"><%=HTML.encodeTags(cc.getMessage())%></div>
       <%
       cc.setMessage(null);
@@ -636 +569 @@
       Formatter<Number> numberFormatter = FormatterFactory.getNumberFormatter(sc);
       %>
-
-    <tbl:table 
-      id="spotdata" 
-       
-      columns="<%=cc.getSetting("columns")%>"
-      sortby="<%=cc.getSortProperty()%>" 
-      direction="<%=cc.getSortDirection()%>"
-      title="<%=title%>"
-      action="index.jsp"
-      sc="<%=sc%>"
-      item="<%=itemType%>"
-      subcontext="<%=subContext%>"
-      >
-      <tbl:hidden 
-        name="bioassayset_id" 
-        value="<%=String.valueOf(bioAssaySetId)%>" 
-      />
-      <%
-      for (AnnotationType at : selectedAnnotationTypes.keySet())
-      {
-        %>
-        <tbl:columndef
-          id="<%="annotation." + at.getId()%>"
-          title="<%=HTML.encodeTags(at.getName()) %>"
-          show="always"
-        />
-        <%
-      }
-      %>
-      <tbl:columndef
-        id="bioassay"
-        property="COLUMN"
-        title="Bioassay"
-        show="always"
-        sortable="true"
-      />
-      <tbl:columndef
-        id="position"
-        property="POSITION"
-        title="Position"
-        show="<%=isAveraging ? "never" : "always" %>"
-        sortable="true"
-      />
-      <tbl:columndef
-        id="count"
-        title="Count"
-        show="<%=isAveraging ? "always" : "never" %>"
-      />
-      <%
-      for (int ch = 1; ch <= channels; ++ch)
-      {
-        %>
-        <tbl:columndef
-          id="<%="ch"+ch%>"
-          property="<%="%"+ch%>"
-          datatype="float"
-          title="<%="Ch " + ch%>"
-          tooltip="<%=transform.isTransformed() ? transform.toString() : null %>"
-          sortable="true"
-          filterable="true"
-          exportable="true"
-          formatter="<%=numberFormatter%>"
-        />
-        <%
-      }
-      %>
-      <%
-      for (TableColumn tc : spotColumns)
-      {
-        %>
-        <tbl:columndef
-          id="<%=tc.getId()%>"
-          property="<%=tc.getProperty()%>"
-          datatype="<%=tc.getDatatype().getStringValue()%>"
-          title="<%=HTML.encodeTags(tc.getTitle())%>"
-          sortable="<%=tc.getSortable()%>"
-          filterable="<%=tc.getFilterable()%>"
-          exportable="<%=tc.getExportable()%>"
-          show="<%=!isAveraging || tc.isAveragable() ? tc.getShow() : "never"%>"
-          formatter="<%=tc.getFormatter()%>"
-        />
-        <%
-      }
-      %>
+      <form name="spotIndex" action="index.jsp" method="post">
+      <input type="hidden" name="ID" value="<%=ID%>">
+      <input type="hidden" name="bioassayset_id" value="<%=bioAssaySetId%>">
+      <input type="hidden" name="cmd" value="SetSpotIndex">
+      <tbl:toolbar subclass="topborder">
+        <tbl:label style="padding: 0px 2px 0px 6px;">
+        Current spot
+        <input name="newSpotIndex" type="text" class="text" value="<%=positionIndex == -1 ? "all" : positionIndex == -2 ? "avg" : String.valueOf(positionIndex+1)%>" 
+          onkeypress="return Numbers.integerOnly(event, true, validateSpotIndex)"
+          size="6" maxlength="8" title="Enter a number between 1 and <%=matchingPositions%>">
+          of <%=matchingPositions%>
         
-      <tbl:toolbar>
+          <%
+          if (positionIndex == 0)
+          {
+            %>
+            <base:icon image="first_gray.gif" />
+            <%
+          }
+          else
+          {
+            %>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=0"
+              title="Go the first position"><base:icon image="first.gif" /></a>
+            <%
+          }
+          if (positionIndex <= 0)
+          {
+            %>
+            <base:icon image="previous_gray.gif" />
+            <%
+          }
+          else
+          {
+            %>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=<%=positionIndex-1%>"
+              title="Go the previous position"><base:icon image="previous.gif" /></a>
+            <%
+          }
+          %>
+          &nbsp;&nbsp;
+          <%
+          if (positionIndex == matchingPositions - 1 || positionIndex < 0)
+          {
+            %>
+            <base:icon image="next_gray.gif" />
+            <%
+          }
+          else
+          {
+            %>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=<%=positionIndex+1%>"
+              title="Go the next position"><base:icon image="next.gif" /></a>
+            <%
+          }
+          if (positionIndex == matchingPositions - 1)
+          {
+            %>
+            <base:icon image="last_gray.gif" />
+            <%
+          }
+          else
+          {
+            %>
+            <a href="index.jsp?ID=<%=ID%>&cmd=SetSpotIndex&bioassayset_id=<%=bioAssaySetId%>&spotIndex=<%=matchingPositions-1%>"
+              title="Go the last position"><base:icon image="last.gif" /></a>
+            <%
+          }
+          %>
+          [ <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"
+            title="Calculate average values for each bioassay">avg</a>
+          ]
+        </tbl:label>
         <tbl:button 
           image="columns.gif" 
@@ -735 +657 @@
         />
       </tbl:toolbar>
-      <tbl:data>
-        <tbl:columns />
-        <tbl:rows>
+      </form>
+      
+      <tbl:table 
+        id="spotdata" 
+        columns="<%=cc.getSetting("columns")%>"
+        sortby="<%=cc.getSortProperty()%>" 
+        direction="<%=cc.getSortDirection()%>"
+        title="<%=title%>"
+        action="index.jsp"
+        sc="<%=sc%>"
+        item="<%=itemType%>"
+        subcontext="<%=subContext%>"
+        >
+        <tbl:hidden 
+          name="bioassayset_id" 
+          value="<%=String.valueOf(bioAssaySetId)%>" 
+        />
         <%
-        int index = 0;
-        float[] intensity = new float[channels+1];
-        while (spotData.hasNext())
+        for (AnnotationType at : selectedAnnotationTypes.keySet())
         {
-          SqlResult item = spotData.next();
-          index++;
-          BioAssay bioAssay = explorer.getBioAssay(dc, item.getShort(1));
-          for (int ch = 1; ch <= channels; ++ch)
-          {
-            intensity[ch] = item.getFloat(2+ch);
-          }
           %>
-          <tbl:row>
-            <%
-            for (Map.Entry<AnnotationType, AnnotationSummary> entry : selectedAnnotationTypes.entrySet())
+          <tbl:columndef
+            id="<%="annotation." + at.getId()%>"
+            title="<%=HTML.encodeTags(at.getName()) %>"
+            show="always"
+          />
+          <%
+        }
+        %>
+        <tbl:columndef
+          id="bioassay"
+          property="COLUMN"
+          title="Bioassay"
+          show="always"
+          sortable="true"
+        />
+        <tbl:columndef
+          id="position"
+          property="POSITION"
+          title="Position"
+          show="<%=isAveraging ? "never" : "always" %>"
+          sortable="true"
+        />
+        <tbl:columndef
+          id="count"
+          title="Count"
+          show="<%=isAveraging ? "always" : "never" %>"
+        />
+        <%
+        for (int ch = 1; ch <= channels; ++ch)
+        {
+          %>
+          <tbl:columndef
+            id="<%="ch"+ch%>"
+            property="<%="%"+ch%>"
+            datatype="float"
+            title="<%="Ch " + ch%>"
+            tooltip="<%=transform.isTransformed() ? transform.toString() : null %>"
+            sortable="true"
+            filterable="true"
+            exportable="true"
+            formatter="<%=numberFormatter%>"
+          />
+          <%
+        }
+        %>
+        <%
+        for (TableColumn tc : spotColumns)
+        {
+          %>
+          <tbl:columndef
+            id="<%=tc.getId()%>"
+            property="<%=tc.getProperty()%>"
+            datatype="<%=tc.getDatatype().getStringValue()%>"
+            title="<%=HTML.encodeTags(tc.getTitle())%>"
+            sortable="<%=tc.getSortable()%>"
+            filterable="<%=tc.getFilterable()%>"
+            exportable="<%=tc.getExportable()%>"
+            show="<%=!isAveraging || tc.isAveragable() ? tc.getShow() : "never"%>"
+            formatter="<%=tc.getFormatter()%>"
+          />
+          <%
+        }
+        %>
+        <tbl:data style="border-left: 0px; border-right: 0px;">
+          <tbl:headers>
+            <tbl:headers>
+              <tbl:columnheaders />
+            </tbl:headers>
+          </tbl:headers>
+          <tbl:rows>
+          <%
+          int index = 0;
+          float[] intensity = new float[channels+1];
+          while (spotData.hasNext())
+          {
+            SqlResult item = spotData.next();
+            index++;
+            BioAssay bioAssay = explorer.getBioAssay(dc, item.getShort(1));
+            for (int ch = 1; ch <= channels; ++ch)
             {
-              AnnotationType at = entry.getKey();
-              AnnotationGroup annotationGroup = entry.getValue().getAnnotationGroup(bioAssay.getDataCubeColumnNo());
-              String allValues = annotationGroup.getTitle();
-              if (hasRatio)
+              intensity[ch] = item.getFloat(2+ch);
+            }
+            %>
+            <tbl:row>
+              <%
+              for (Map.Entry<AnnotationType, AnnotationSummary> entry : selectedAnnotationTypes.entrySet())
               {
-                float logRatio = (float)(Math.log(transform.unTransform(intensity[1]) / transform.unTransform(intensity[2])));
-                annotationGroup.addStatistics("logratio", logRatio);
-                annotationGroup.addStatistics("logratio2", logRatio * logRatio);
+                AnnotationType at = entry.getKey();
+                AnnotationGroup annotationGroup = entry.getValue().getAnnotationGroup(bioAssay.getDataCubeColumnNo());
+                String allValues = annotationGroup.getTitle();
+                if (hasRatio)
+                {
+                  float logRatio = (float)(Math.log(transform.unTransform(intensity[1]) / transform.unTransform(intensity[2])));
+                  annotationGroup.addStatistics("logratio", logRatio);
+                  annotationGroup.addStatistics("logratio2", logRatio * logRatio);
+                }
+                for (int ch = 1; ch <= channels; ++ch)
+                {
+                  annotationGroup.addValue(ch, (float)transform.unTransform(intensity[ch]));
+                }
+                %>
+                <tbl:cell column="<%="annotation."+at.getId()%>" style="<%="background: "+annotationGroup.getColor()+";"%>">
+                <%=allValues%>
+                </tbl:cell>
+                <%
               }
+              %>
+              <tbl:cell column="bioassay"><%=Base.getLinkedName(ID, bioAssay, false, true)%></tbl:cell>
+              <tbl:cell column="position"><%=item.getInt(2)%></tbl:cell>
+              <tbl:cell column="count"><%=item.getInt(2)%></tbl:cell>
+              <%
               for (int ch = 1; ch <= channels; ++ch)
               {
-                annotationGroup.addValue(ch, (float)transform.unTransform(intensity[ch]));
+                %>
+                <tbl:cell column="<%="ch" + ch%>" value="<%=intensity[ch]%>" />
+                <%
               }
               %>
-              <tbl:cell column="<%="annotation."+at.getId()%>" style="<%="background: "+annotationGroup.getColor()+";"%>">
-              <%=allValues%>
-              </tbl:cell>
               <%
-            }
-            %>
-            <tbl:cell column="bioassay"><%=Base.getLinkedName(ID, bioAssay, false, true)%></tbl:cell>
-            <tbl:cell column="position"><%=item.getInt(2)%></tbl:cell>
-            <tbl:cell column="count"><%=item.getInt(2)%></tbl:cell>
-            <%
-            for (int ch = 1; ch <= channels; ++ch)
-            {
+              int colIndex = 3 + channels;
+              for (String columnId : selected.selectedIds)
+              {
+                %>
+                <tbl:cell column="<%=columnId%>" value="<%=item.getObject(colIndex++)%>" />
+                <%
+              }
               %>
-              <tbl:cell column="<%="ch" + ch%>" value="<%=intensity[ch]%>" />
-              <%
-            }
-            %>
-            <%
-            int colIndex = 3 + channels;
-            for (String columnId : selected.selectedIds)
-            {
-              %>
-              <tbl:cell column="<%=columnId%>" value="<%=item.getObject(colIndex++)%>" />
-              <%
-            }
-            %>
-          </tbl:row>
-          <%
-        }
-      %>
-      </tbl:rows>
-      </tbl:data>
+            </tbl:row>
+            <%
+          }
+        %>
+        </tbl:rows>
+        </tbl:data>
       </tbl:table>
-      </div>
       <%
       }
@@ -814 +823 @@
           AnnotationType at = entry.getKey();
           AnnotationSummary summary = entry.getValue();
-          %>
-          <%
-          for (AnnotationGroup ag : summary.getAnnotationGroups())
-          {
-            for (int ch = 1; ch <= channels; ++ch)
+          if (summary != null)
+          {
+            for (AnnotationGroup ag : summary.getAnnotationGroups())
             {
+              for (int ch = 1; ch <= channels; ++ch)
+              {
+                %>
+                var div = document.getElementById('mean.<%=at.getId()%>.<%=ag.getId()%>.ch<%=ch%>');
+                div.innerHTML = '<%=Values.formatNumber(ag.getMean(ch), 2)%>';
+                <%
+              }
               %>
-              var div = document.getElementById('mean.<%=at.getId()%>.<%=ag.getId()%>.ch<%=ch%>');
-              div.innerHTML = '<%=Values.formatNumber(ag.getMean(ch), 2)%>';
+              var div = document.getElementById('count.<%=at.getId()%>.<%=ag.getId()%>');
+              div.innerHTML = '<%=ag.getCount(1)%>';
               <%
-            }
-            %>
-            var div = document.getElementById('count.<%=at.getId()%>.<%=ag.getId()%>');
-            div.innerHTML = '<%=ag.getCount(1)%>';
-            <%
-            if (hasRatio)
-            {
-              float r = ag.getStatistics("logratio");
-              int count = ag.getCount(1);
-              float gMean = count > 0 ? (float)Math.exp(r / count) : Float.NaN;
-              float sd = count > 1 ? 
-                (float)Math.sqrt((ag.getStatistics("logratio2") - r * (r / count))/(count-1))
-                : Float.NaN;
-              %>
-              var div = document.getElementById('gmean.<%=at.getId()%>.<%=ag.getId()%>');
-              div.innerHTML = '<%=Values.formatNumber(gMean, 2)%>';
-              var div = document.getElementById('sd.<%=at.getId()%>.<%=ag.getId()%>');
-              div.innerHTML = '<%=Values.formatNumber(sd, 2)%>';
-              <%
+              if (hasRatio)
+              {
+                float r = ag.getStatistics("logratio");
+                int count = ag.getCount(1);
+                float gMean = count > 0 ? (float)Math.exp(r / count) : Float.NaN;
+                float sd = count > 1 ? 
+                  (float)Math.sqrt((ag.getStatistics("logratio2") - r * (r / count))/(count-1))
+                  : Float.NaN;
+                %>
+                var div = document.getElementById('gmean.<%=at.getId()%>.<%=ag.getId()%>');
+                div.innerHTML = '<%=Values.formatNumber(gMean, 2)%>';
+                var div = document.getElementById('sd.<%=at.getId()%>.<%=ag.getId()%>');
+                div.innerHTML = '<%=Values.formatNumber(sd, 2)%>';
+                <%
+              }
             }
           }
@@ -865 +875 @@
       Main.onLoad(init);
       </script>
-      
-      </t:tab>
-      </t:tabcontrol>
+      <%
+    }
+    %>
+    </t:tab>
+    </t:tabcontrol>
 
   </base:body>

trunk/www/views/experiments/extravalues/view_extravalue.jsp

@@ -175 +175 @@
   </base:head>
   <base:body>
-    <p>
-    <p:path>
-      <p:pathelement title="Experiments" href="<%="../index.jsp?ID="+ID%>" />
-      <p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
-        href="<%="../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experimentId%>" />
-      <p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" 
-        href="<%="../bioassaysets/index.jsp?ID="+ID+"&cmd=ViewItem&experiement_id="+experimentId+"&item_id="+bioAssaySet.getId()%>" />
-      <p:pathelement title="<%=HTML.encodeTags(extraValueType == null ? extraValue.getValueType().toString() : extraValueType.getName()) %>" />
-    </p:path>
+    <p:path><p:pathelement 
+      title="Experiments" href="<%="../index.jsp?ID="+ID%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
+        href="<%="../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experimentId%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" 
+        href="<%="../bioassaysets/index.jsp?ID="+ID+"&cmd=ViewItem&experiement_id="+experimentId+"&item_id="+bioAssaySet.getId()%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(extraValueType == null ? extraValue.getValueType().toString() : extraValueType.getName()) %>" 
+      /></p:path>
     
-    <t:tabcontrol id="view" remember="false">
+    <t:tabcontrol 
+      id="view" 
+      subclass="content mastertabcontrol"
+      remember="false">
     <t:tab id="properties" title="Properties">
-    
-    <tbl:toolbar
-      >
-      <tbl:button 
-        disabled="<%=deletePermission ? false : true%>" 
-        image="delete.gif" 
-        onclick="deleteItem()" 
-        title="Delete"
-        tooltip="<%=deletePermission ? "Delete this extra value" : "You do not have permission to delete this extra value"%>" 
-      />
-      <tbl:button 
-        disabled="<%=writePermission ? false : true%>" 
-        image="<%=writePermission ? "copy.gif" : "copy_disabled.gif"%>" 
-        onclick="<%=job == null ? "" : "copyJob('" + job.getId() + "')"%>" 
-        title="Copy&hellip;"
-        visible="<%=job != null && plugin != null && plugin.isInteractive() %>"
-        tooltip="<%=writePermission ? "Copy this transformation" : "You do not have permission to copy this transformation"%>" 
-      />
-      <tbl:button 
-        image="import.gif" 
-        onclick="<%="runPlugin(" + itemId + ", 'ImportItem')"%>" 
-        title="Import&hellip;" 
-        tooltip="Import data" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
-      />
-      <tbl:button 
-        image="export.gif" 
-        onclick="<%="runPlugin(" + itemId + ", 'ExportItem')"%>" 
-        title="Export&hellip;" 
-        tooltip="Export data" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
-      />
-      <tbl:button 
-        image="runplugin.gif" 
-        onclick="<%="runPlugin(" + itemId + ", 'RunPlugin')"%>"
-        title="Run plugin&hellip;" 
-        tooltip="Run a plugin" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
-      />
-      <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
-        wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
-      <tbl:button
-        image="help.png"
-        onclick="<%="Main.openHelp('" + ID +"', 'extravalue.view.properties')"%>"
-        title="Help&hellip;"
-        tooltip="Get help about this page"
-      />
-      </tbl:toolbar>
-      
-    <div class="boxedbottom">
-      <div class="itemstatus">Permissions on this item: <i><%=PermissionUtil.getFullPermissionNames(extraValue)%></i></div>
-      
-      <table width="100%">
-      <tr >
-      <td width="50%">
-        <h4>Extra value</h4>
-        <table class="form" cellspacing=0>
+      <div>
+      <table class="fullform">
+      <tr>
+        <th class="itemstatus">
+        </th>
+        <td style="padding: 0px;">
+          <tbl:toolbar subclass="bottomborder">
+            <tbl:button 
+              disabled="<%=deletePermission ? false : true%>" 
+              image="delete.gif" 
+              onclick="deleteItem()" 
+              title="Delete"
+              tooltip="<%=deletePermission ? "Delete this extra value" : "You do not have permission to delete this extra value"%>" 
+            />
+            <tbl:button 
+              disabled="<%=writePermission ? false : true%>" 
+              image="copy.gif" 
+              onclick="<%=job == null ? "" : "copyJob('" + job.getId() + "')"%>" 
+              title="Copy&hellip;"
+              visible="<%=job != null && plugin != null && plugin.isInteractive() %>"
+              tooltip="<%=writePermission ? "Copy this transformation" : "You do not have permission to copy this transformation"%>" 
+            />
+            <tbl:button 
+              image="import.gif" 
+              onclick="<%="runPlugin(" + itemId + ", 'ImportItem')"%>" 
+              title="Import&hellip;" 
+              tooltip="Import data" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
+            />
+            <tbl:button 
+              image="export.gif" 
+              onclick="<%="runPlugin(" + itemId + ", 'ExportItem')"%>" 
+              title="Export&hellip;" 
+              tooltip="Export data" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
+            />
+            <tbl:button 
+              image="runplugin.gif" 
+              onclick="<%="runPlugin(" + itemId + ", 'RunPlugin')"%>"
+              title="Run plugin&hellip;" 
+              tooltip="Run a plugin" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
+            />
+            <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
+              wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
+            <tbl:button
+              image="help.png"
+              onclick="<%="Main.openHelp('" + ID +"', 'extravalue.view.properties')"%>"
+              title="Help&hellip;"
+              tooltip="Get help about this page"
+            />
+          </tbl:toolbar>
+        </td>
+      </tr>
+    </table>
+    <table style="width: 100%; height: 16em;" class="bottomborder">
+    <tr valign="top">
+      <td style="width: 50%; height: 100%;">
+      <table class="fullform" >
         <%
         if (extraValueType == null)
@@ -249 +253 @@
           %>
           <tr>
-            <td class="prompt">Type</td>
+            <th>Type</th>
             <td><%=extraValue.getValueType()%></td>
           </tr>
@@ -258 +262 @@
           %>
           <tr>
-            <td class="prompt">Name</td>
+            <th>Name</th>
             <td><%=Base.getLinkedName(ID, extraValueType, !readExtraValueType, writePermission)%></td>
           </tr>
@@ -265 +269 @@
         %>
         <tr>
-          <td class="prompt">Bioassay set</td>
+          <th>Bioassay set</th>
           <td><%=Base.getLinkedName(ID, bioAssaySet, false, writePermission)%></td>
         </tr>
         <tr>
-          <td class="prompt">Experiment</td>
+          <th>Experiment</th>
           <td><%=Base.getLinkedName(ID, experiment, false, writePermission)%>
           (<%=experiment.getRawDataType()%>)</td>
         </tr>
         <tr>
-          <td class="prompt">Values</td>
+          <th>Values</th>
           <td>db: <%=extraValue.getNumValues()%>; file: <%=extraValue.getNumFileValues()%></td>
         </tr>
         <tr>
-          <td class="prompt">Description</td>
+          <th>Description</th>
           <td><%=HTML.niceFormat(extraValueType != null ? extraValueType.getDescription() : "")%></td>
         </tr>
-        </table>
-        
-        <h4>Job</h4>
-        <table class="form" cellspacing=0>
-        <tr>
-          <td class="prompt">Job</td>
+        <tr>
+          <th>Job</th>
           <td><%=Base.getLinkedName(ID, job, !readJob, false)%></td>
         </tr>
         <tr >
-          <td class="prompt">Started</td>
+          <th class="subprompt">- started</td>
           <td>
             <%=job == null ? "" : dateTimeFormatter.format(job.getStarted())%>
@@ -296 +296 @@
         </tr>
         <tr >
-          <td class="prompt">Ended</td>
+          <th class="subprompt">- ended</td>
           <td>
             <%=job == null ? "" : dateTimeFormatter.format(job.getEnded())%>
           </td>
         </tr>
-        <tr >
-          <td class="prompt">Server</td>
+        <tr class="dynamic">
+          <th class="subprompt">- server</td>
           <td>
             <%=job == null ? "" : HTML.encodeTags(job.getServer())%>
@@ -309 +309 @@
         </table>
       </td>
-      <td width="50%">
-        <h4>Plugin &amp; parameters</h4>
-        <table class="form" cellspacing=0>
-        <tr>
-          <td class="prompt">Plugin</td>
+      <td style="width: 50%; height: 100%;" class="leftborder">
+        <table class="fullform" >
+        <tr>
+          <th>Plugin</th>
           <td><%=Base.getLinkedName(ID, plugin, 
               !readPlugin, plugin != null && plugin.hasPermission(Permission.WRITE))%></td>
         </tr>
         <tr>
-          <td class="prompt">Plugin configuration</td>
+          <th>Plugin configuration</th>
           <td><%=Base.getLinkedName(ID, configuration, !readConfiguration, 
             configuration != null && configuration.hasPermission(Permission.WRITE))%></td>
         </tr>
+        <tbody class="sectionheader">
+          <tr>
+            <th colspan="2">Plugin parameters</th>
+          </tr>
+        </tbody>
         <%
         if (job != null)
@@ -380 +384 @@
             %>
             <tr>
-            <td class="prompt"><span title="<%=description%>"><%=name%></span></td>
-              <td>
-                <%=displayValue%>
-              </td>
+            <th class="subprompt">- <span title="<%=description%>"><%=name%></span></td>
+              <td><%=displayValue%></td>
             </tr>
             <%
@@ -389 +391 @@
         }
         %>
+        <tr class="dynamic">
+          <th></th>
+          <td></td>
+        </tr>
         </table>
 
@@ -394 +400 @@
       </tr>
       </table>
-      
       </div>
     </t:tab>

trunk/www/views/experiments/transformations/view_transformation.jsp

@@ -164 +164 @@
   </base:head>
   <base:body>
-    <p>
-    <p:path>
-      <p:pathelement title="Experiments" href="<%="../index.jsp?ID="+ID%>" />
-      <p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
-        href="<%="../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experimentId%>" />
-      <p:pathelement title="<%=HTML.encodeTags(transformation.getName())%>" />
-    </p:path>
+    <p:path><p:pathelement 
+      title="Experiments" href="<%="../index.jsp?ID="+ID%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
+        href="<%="../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experimentId%>" 
+      /><p:pathelement title="<%=HTML.encodeTags(transformation.getName())%>" 
+      /></p:path>
     
-    <t:tabcontrol id="main" active="<%=tabId%>" switch="switchTab">
+    <t:tabcontrol 
+      id="main" 
+      subclass="content mastertabcontrol"
+      active="<%=tabId%>" switch="switchTab">
     <t:tab id="properties" title="Properties">
-    
-    <tbl:toolbar
-      >
-      <tbl:button 
-        disabled="<%=writePermission ? false : true%>" 
-        image="edit.gif" 
-        onclick="editItem()" 
-        title="Edit&hellip;" 
-        tooltip="<%=writePermission ? "Edit this transformation" : "You do not have permission to edit this transformation"%>" 
-      />
-      <tbl:button 
-        disabled="<%=deletePermission ? false : true%>" 
-        image="delete.gif" 
-        onclick="deleteItem()" 
-        title="Delete"
-        visible="<%=!transformation.isRemoved()%>"
-        tooltip="<%=deletePermission ? "Delete this transformation" : "You do not have permission to delete this transformation"%>" 
-      />
-      <tbl:button 
-        disabled="<%=writePermission ? false : true%>" 
-        image="restore.gif" 
-        onclick="restoreItem()" 
-        title="Restore"
-        visible="<%=transformation.isRemoved()%>"
-        tooltip="<%=writePermission ? "Restore this transformation" : "You do not have permission to restore this transformation"%>" 
-      />
-      <tbl:button 
-        disabled="<%=writePermission ? false : true%>" 
-        image="<%=writePermission ? "copy.gif" : "copy_disabled.gif"%>" 
-        onclick="<%=job == null ? "" : "copyJob('" + job.getId() + "')"%>" 
-        title="Copy&hellip;"
-        visible="<%=job != null && plugin != null && plugin.isInteractive() %>"
-        tooltip="<%=writePermission ? "Copy this transformation" : "You do not have permission to copy this transformation"%>" 
-      />
-      <tbl:button 
-        image="import.gif" 
-        onclick="runItemPlugin('ImportItem')" 
-        title="Import&hellip;" 
-        tooltip="Import data" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
-      />
-      <tbl:button 
-        image="export.gif" 
-        onclick="runItemPlugin('ExportItem')" 
-        title="Export&hellip;" 
-        tooltip="Export data" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
-      />
-      <tbl:button 
-        image="runplugin.gif" 
-        onclick="runItemPlugin('RunPlugin')" 
-        title="Run plugin&hellip;" 
-        tooltip="Run a plugin" 
-        visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
-      />
-      <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
-        wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
-      <tbl:button
-        image="help.png"
-        onclick="<%="Main.openHelp('" + ID +"', 'transformation.view.properties')"%>"
-        title="Help&hellip;"
-        tooltip="Get help about this page"
-      />
-      </tbl:toolbar>
-    <div class="boxedbottom">
-      <div class="itemstatus">Permissions on this item: <i><%=PermissionUtil.getFullPermissionNames(transformation)%></i></div>
-      <%
-      if (transformation.isRemoved())
-      {
-        %>
-        <div class="itemstatus">
-          <base:icon image="deleted.gif" 
-            visible="<%=transformation.isRemoved()%>"> This item has been flagged for deletion<br></base:icon>
-        </div>
-        <%
-      }
-      %>
-      
-      <table width="100%">
-      <tr >
-      <td width="50%">
-        <h4>Transformation</h4>
-        <table class="form" cellspacing=0>
-        <tr>
-          <td class="prompt">Name</td>
+      <div>
+      <table class="fullform">
+      <tr>
+        <th class="itemstatus">
+          <base:icon 
+            image="deleted.gif"
+            onclick="deleteItemPermanently()"
+            tooltip="This item has been flagged for deletion. Click to delete it now."
+            enabled="<%=deletePermission %>"
+            visible="<%=transformation.isRemoved()%>" 
+          />
+        </th>
+        <td style="padding: 0px;">
+          <tbl:toolbar subclass="bottomborder">
+            <tbl:button 
+              disabled="<%=writePermission ? false : true%>" 
+              image="edit.gif" 
+              onclick="editItem()" 
+              title="Edit&hellip;" 
+              tooltip="<%=writePermission ? "Edit this transformation" : "You do not have permission to edit this transformation"%>" 
+            />
+            <tbl:button 
+              disabled="<%=deletePermission ? false : true%>" 
+              image="delete.gif" 
+              onclick="deleteItem()" 
+              title="Delete"
+              visible="<%=!transformation.isRemoved()%>"
+              tooltip="<%=deletePermission ? "Delete this transformation" : "You do not have permission to delete this transformation"%>" 
+            />
+            <tbl:button 
+              disabled="<%=writePermission ? false : true%>" 
+              image="restore.gif" 
+              onclick="restoreItem()" 
+              title="Restore"
+              visible="<%=transformation.isRemoved()%>"
+              tooltip="<%=writePermission ? "Restore this transformation" : "You do not have permission to restore this transformation"%>" 
+            />
+            <tbl:button 
+              disabled="<%=writePermission ? false : true%>" 
+              image="<%=writePermission ? "copy.gif" : "copy_disabled.gif"%>" 
+              onclick="<%=job == null ? "" : "copyJob('" + job.getId() + "')"%>" 
+              title="Copy&hellip;"
+              visible="<%=job != null && plugin != null && plugin.isInteractive() %>"
+              tooltip="<%=writePermission ? "Copy this transformation" : "You do not have permission to copy this transformation"%>" 
+            />
+            <tbl:button 
+              image="import.gif" 
+              onclick="runItemPlugin('ImportItem')" 
+              title="Import&hellip;" 
+              tooltip="Import data" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
+            />
+            <tbl:button 
+              image="export.gif" 
+              onclick="runItemPlugin('ExportItem')" 
+              title="Export&hellip;" 
+              tooltip="Export data" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
+            />
+            <tbl:button 
+              image="runplugin.gif" 
+              onclick="runItemPlugin('RunPlugin')" 
+              title="Run plugin&hellip;" 
+              tooltip="Run a plugin" 
+              visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
+            />
+            <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" 
+              wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
+            <tbl:button
+              image="help.png"
+              onclick="<%="Main.openHelp('" + ID +"', 'transformation.view.properties')"%>"
+              title="Help&hellip;"
+              tooltip="Get help about this page"
+            />
+          </tbl:toolbar>
+        </td>
+      </tr>
+      </table>
+      <table style="width: 100%; height: 15em;" class="bottomborder">
+      <tr valign="top">
+        <td style="width: 50%; height: 100%;">
+        <table class="fullform" >
+        <tr>
+          <th>Name</th>
           <td><%=HTML.encodeTags(transformation.getName())%></td>
         </tr>
         <tr>
-          <td class="prompt">Experiment</td>
+          <th>Experiment</th>
           <td><%=Base.getLinkedName(ID, experiment, false, writePermission)%></td>
         </tr>
         <tr>
-          <td class="prompt">Description</td>
+          <th>Description</th>
           <td><%=HTML.niceFormat(transformation.getDescription())%></td>
         </tr>
-        </table>
-        
-        <h4>Job</h4>
-        <table class="form" cellspacing=0>
-        <tr>
-          <td class="prompt">Job</td>
+        <tr>
+          <th>Job</th>
           <td><%=Base.getLinkedName(ID, job, !readJob, false)%></td>
         </tr>
-        <tr >
-          <td class="prompt">Started</td>
+        <tr>
+          <th class="subprompt">- started</th>
           <td>
             <%=job == null ? "" : dateTimeFormatter.format(job.getStarted())%>
@@ -284 +281 @@
         </tr>
         <tr >
-          <td class="prompt">Ended</td>
+          <th class="subprompt">- ended</th>
           <td>
             <%=job == null ? "" : dateTimeFormatter.format(job.getEnded())%>
           </td>
         </tr>
-        <tr >
-          <td class="prompt">Server</td>
+        <tr class="dynamic">
+          <th class="subprompt">- server</th>
           <td>
             <%=job == null ? "" : HTML.encodeTags(job.getServer())%>
@@ -297 +294 @@
         </table>
       </td>
-      <td width="50%">
-        <h4>Plugin &amp; parameters</h4>
-        <table class="form" cellspacing=0>
-        <tr>
-          <td class="prompt">Plugin</td>
+      <td style="width: 50%; height: 100%;" class="leftborder">
+        <table class="fullform" >
+        <tr>
+          <th>Plugin</th>
           <td><%=Base.getLinkedName(ID, plugin, 
               !readPlugin, plugin != null && plugin.hasPermission(Permission.WRITE))%></td>
         </tr>
         <tr>
-          <td class="prompt">Plugin configuration</td>
+          <th>Plugin configuration</th>
           <td><%=Base.getLinkedName(ID, configuration, !readConfiguration, 
             configuration != null && configuration.hasPermission(Permission.WRITE))%></td>
         </tr>
+        <tbody class="sectionheader">
+          <tr>
+            <th colspan="2">Plugin parameters</th>
+          </tr>
+        </tbody>
         <%
         if (job != null)
@@ -368 +369 @@
             %>
             <tr>
-              <td class="prompt"><span title="<%=description%>"><%=name%></span></td>
+              <th class="subprompt"><span title="<%=description%>">- <%=name%></span></th>
               <td>
                 <%=displayValue%>
@@ -377 +378 @@
         }
         %>
+        <tr class="dynamic">
+          <th></th>
+          <td></td>
+        </tr>
         </table>
       </td>
@@ -389 +394 @@
       </jsp:include>
       
-      <h4 class="docked">Analysis subtree</h4>
-      <jsp:include page="../bioassaysets/analysis_tree.jsp">
-        <jsp:param name="ID" value="<%=ID%>" />
-        <jsp:param name="experiment_id" value="<%=experimentId%>" />
-        <jsp:param name="transformation_id" value="<%=itemId%>" />
-      </jsp:include>
-      </div>
+      <base:section id="anaysis" title="Analysis subtree" context="<%=cc%>">
+        <jsp:include page="../bioassaysets/analysis_tree.jsp">
+          <jsp:param name="ID" value="<%=ID%>" />
+          <jsp:param name="experiment_id" value="<%=experimentId%>" />
+          <jsp:param name="transformation_id" value="<%=itemId%>" />
+        </jsp:include>
+      </base:section>
       </t:tab>
       </t:tabcontrol>