Changeset 3558

Timestamp:

Jul 16, 2007, 9:44:02 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #669

Location:

trunk

Files:

• src/core/net/sf/basedb/core/Formula.java (modified) (6 diffs)
• www/admin/extravaluetypes/edit_extravaluetype.jsp (modified) (6 diffs)
• www/admin/extravaluetypes/index.jsp (modified) (2 diffs)
• www/admin/extravaluetypes/list_extravaluetypes.jsp (modified) (5 diffs)
• www/admin/extravaluetypes/view_extravaluetype.jsp (modified) (1 diff)
• www/include/scripts/main.js (modified) (2 diffs)
• www/views/formulas/edit_formula.jsp (modified) (8 diffs)
• www/views/formulas/index.jsp (modified) (1 diff)
• www/views/formulas/list_formulas.jsp (modified) (4 diffs)
• www/views/formulas/view_formula.jsp (modified) (1 diff)

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

@@ -487 +487 @@
       is typically used to create a root bioassay set from raw data.
     */
-    INTENSITY_EXPRESSION(1, "Intensity expression", false)
+    INTENSITY_EXPRESSION(1, "Intensity expression", false, false)
     {
       /**
@@ -519 +519 @@
       bioassay set into a child bioassay set.
     */
-    INTENSITY_TRANSFORMATION(2, "Intensity transformation", false)    
+    INTENSITY_TRANSFORMATION(2, "Intensity transformation", false, false)   
     {
       /**
@@ -561 +561 @@
       The formula can also be used to calculate extra values for a bioassay set.
     */
-    COLUMN_EXPRESSION(3, "Column expression", true)
+    COLUMN_EXPRESSION(3, "Column expression", true, true)
     {
       /**
@@ -584 +584 @@
       to create a filtered bioassay set.
     */
-    COLUMN_RESTRICTION(4, "Column restriction", false)
+    COLUMN_RESTRICTION(4, "Column restriction", false, false)
     {
       /**
@@ -631 +631 @@
     private final String displayValue;
     private final boolean canUseColoring;
-    
-    private Type(int value, String displayValue, boolean canUseColoring)
+    private final boolean supportsAverage;
+    
+    private Type(int value, String displayValue, boolean canUseColoring, boolean supportsAverage)
     {
       this.value = value;
       this.displayValue = displayValue;
       this.canUseColoring = canUseColoring;
+      this.supportsAverage = supportsAverage;
     }
     
@@ -661 +663 @@
     {
       return canUseColoring;
+    }
+    
+    /**
+      If a formula of this type can be used in an average expression or not.
+      This is only possible for formulas which create one value.
+      @since 2.4
+    */
+    public boolean supportsAverage()
+    {
+      return supportsAverage;
     }
     

trunk/www/admin/extravaluetypes/edit_extravaluetype.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.ExtraValueType"
+  import="net.sf.basedb.core.Formula"
   import="net.sf.basedb.core.Coloring"
   import="net.sf.basedb.core.PermissionDeniedException"
@@ -55 +56 @@
   ExtraValueType extraValueType = null;
   Coloring coloring = null;
+  Formula.AverageMethod currentAverageMethod = null;
 
   if (itemId == 0)
@@ -60 +62 @@
     title = "Create extra value type";
     cc.removeObject("item");
+    currentAverageMethod = Formula.AverageMethod.fromValue(Values.getInt(cc.getPropertyValue("averageMethod"),
+      Formula.AverageMethod.ARITHMETIC_MEAN.getValue()));
     coloring = new Coloring();
     coloring.setUsingColors(Values.getBoolean(cc.getPropertyValue("coloring.usingColors")));
@@ -70 +74 @@
   {
     extraValueType = ExtraValueType.getById(dc, itemId);
+    currentAverageMethod = extraValueType.getAverageMethod();
     coloring = extraValueType.getColoring();
     cc.setObject("item", extraValueType);
@@ -199 +204 @@
 
     <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
-    <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*200)+"px;"%>" 
+    <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*240)+"px;"%>" 
       position="bottom" remember="<%=extraValueType != null%>">
     <t:tab id="info" title="Extra value type" validate="validateExtraValueType()" 
@@ -242 +247 @@
           }
           %>
+        </td>
+      </tr>
+      <tr>
+        <td class="prompt">Avg. method</td>
+        <td>
+          <select name="averageMethod" class="required">
+          <%
+          for (Formula.AverageMethod method : Formula.AverageMethod.values())
+          {
+            String selected = method == currentAverageMethod ? "selected" : "";
+            %>
+            <option value="<%=method.name()%>" <%=selected%>><%=HTML.encodeTags(method.toString())%>
+            <%
+          }
+          %>
+          </select>
         </td>
       </tr>

trunk/www/admin/extravaluetypes/index.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.ExtraValueType"
+  import="net.sf.basedb.core.Formula"
   import="net.sf.basedb.core.Coloring"
   import="net.sf.basedb.core.ItemQuery"
@@ -143 +144 @@
     extraValueType.setDescription(Values.getStringOrNull(request.getParameter("description")));
     extraValueType.setExternalId(externalId);
+    extraValueType.setAverageMethod(Formula.AverageMethod.valueOf(request.getParameter("averageMethod")));
     Coloring coloring = extraValueType.getColoring();
     coloring.setUsingColors(Values.getBoolean(request.getParameter("use_colors")));

trunk/www/admin/extravaluetypes/list_extravaluetypes.jsp

@@ -31 +31 @@
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ExtraValueType"
+  import="net.sf.basedb.core.Formula"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Include"
@@ -58 +59 @@
 
   private static final Enumeration<String, String> valueTypes = new Enumeration<String, String>();
+  private static final Enumeration<String, String> avgMethods = new Enumeration<String, String>();
   static
   {
@@ -63 +65 @@
     valueTypes.add(Integer.toString(Type.FLOAT.getValue()), Type.FLOAT.toString());
     valueTypes.add(Integer.toString(Type.STRING.getValue()), Type.STRING.toString());
+    for (Formula.AverageMethod m : Formula.AverageMethod.values())
+    {
+      avgMethods.add(Integer.toString(m.getValue()), HTML.encodeTags(m.toString()));
+    }
   }
 
@@ -213 +219 @@
         title="Value type"
         enumeration="<%=valueTypes%>"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
+        id="averageMethod"
+        property="averageMethod"
+        datatype="int"
+        enumeration="<%=avgMethods%>"
+        title="Avg. method"
         sortable="true" 
         filterable="true"
@@ -414 +430 @@
                 <tbl:cell column="externalId"><%=HTML.encodeTags(item.getExternalId())%></tbl:cell>
                 <tbl:cell column="valueType"><%=item.getValueType()%></tbl:cell>
+                <tbl:cell column="averageMethod"><%=item.getAverageMethod().toString()%></tbl:cell>
                 <tbl:cell column="useColors"><%=item.getColoring().isUsingColors() ? "yes" : "no"%></tbl:cell>
                 <tbl:cell column="logarithmic"><%=item.getColoring().isLogarithmic() ? "yes" : "no"%></tbl:cell>

trunk/www/admin/extravaluetypes/view_extravaluetype.jsp

@@ -182 +182 @@
       </tr>
       <tr>
+        <td class="prompt">Avg. method</td>
+        <td><%=extraValueType.getAverageMethod().toString()%></td>
+      </tr>
+      <tr>
         <td class="prompt">Use coloring</td>
         <td>

trunk/www/include/scripts/main.js

@@ -366 +366 @@
     this.controllers['TRANSFORMATION'] = { url:'views/experiments/transformations/index.jsp', width:500, height:300 };
     this.controllers['JOB'] = { url:'views/jobs/index.jsp', width:600, height:440, popup:true, edit:false };
-    this.controllers['FORMULA'] = { url:'views/formulas/index.jsp', width:700, height:460 };
+    this.controllers['FORMULA'] = { url:'views/formulas/index.jsp', width:740, height:500 };
     this.controllers['HYBRIDIZATION'] = { url:'views/hybridizations/index.jsp', width:800, height:500 };
     this.controllers['RAWBIOASSAY'] = { url:'views/rawbioassays/index.jsp', width:800, height:500 };
@@ -421 +421 @@
     this.controllers['USER'] = { url:'admin/users/index.jsp', width:600, height:440 };
     this.controllers['ANYTOANY'] = { url:'common/anytoany/index.jsp', width:500, height:340, popup:true };
-    this.controllers['EXTRAVALUETYPE'] = { url:'admin/extravaluetypes/index.jsp', width:500, height:340 };
+    this.controllers['EXTRAVALUETYPE'] = { url:'admin/extravaluetypes/index.jsp', width:500, height:360 };
     this.controllers['EXTRAVALUE'] = { url:'views/experiments/extravalues/index.jsp', width:500, height:340, edit:false };
   }

trunk/www/views/formulas/edit_formula.jsp

@@ -60 +60 @@
   Formula.Type currentType = null;
   Formula.Parser currentParser = null;
+  Formula.AverageMethod currentAverageMethod = null;
   RawDataType currentRawDataType = null;
   RawDataType defaultRawDataType = null;
@@ -82 +83 @@
     currentParser = Formula.Parser.fromValue(Values.getInt(cc.getPropertyValue("parser"), 
       Formula.Parser.JEP.getValue()));
+    currentAverageMethod = Formula.AverageMethod.fromValue(Values.getInt(cc.getPropertyValue("averageMethod"),
+      Formula.AverageMethod.ARITHMETIC_MEAN.getValue()));
     currentRawDataType = RawDataTypes.getRawDataType(cc.getPropertyValue("rawDataType"));
     if (currentRawDataType == null)
@@ -100 +103 @@
     formula = Formula.getById(dc, itemId);
     currentParser = formula.getParser();
+    currentAverageMethod = formula.getAverageMethod();
     currentType = formula.getFormulaType();
     currentRawDataType = formula.getRawDataType();
@@ -301 +305 @@
   
     var useColors = new Array();
+    var supportsAverage = new Array();
     <%
     for (Formula.Type ft : Formula.Type.values())
@@ -306 +311 @@
       %>
       useColors['<%=ft.name()%>'] = <%=ft.canUseColoring()%>;
+      supportsAverage['<%=ft.name()%>'] = <%=ft.supportsAverage()%>;
       <%
     }
@@ -339 +345 @@
       frm.use_colors.disabled = !use;
       useColorsOnClick();
+      var supportsAvg = supportsAverage[formulaType];
+      frm.averageMethod.disabled = !supportsAvg;
+      if (!supportsAvg) frm.averageMethod.selectedIndex = 0;
     }
     </script>
@@ -348 +357 @@
 
     <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
-    <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*340)+"px;"%>" 
+    <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*380)+"px;"%>" 
       position="bottom"  remember="<%=formula != null%>">
     <t:tab id="info" title="Formula" validate="validateFormula()" helpid="formula.edit">
@@ -454 +463 @@
         </td>
       </tr>
+      <tr>
+        <td class="prompt">Avg. method</td>
+        <td>
+          <select name="averageMethod" class="required">
+          <%
+          for (Formula.AverageMethod method : Formula.AverageMethod.values())
+          {
+            String selected = method == currentAverageMethod ? "selected" : "";
+            %>
+            <option value="<%=method.name()%>" <%=selected%>><%=HTML.encodeTags(method.toString())%>
+            <%
+          }
+          %>
+          </select>
+        </td>
+      </tr>
       
       <tr>

trunk/www/views/formulas/index.jsp

@@ -147 +147 @@
     formula.setDescription(Values.getStringOrNull(request.getParameter("description")));
     formula.setParser(Formula.Parser.valueOf(request.getParameter("parser")));
+    formula.setAverageMethod(Formula.AverageMethod.valueOf(request.getParameter("averageMethod")));
     Formula.Type formulaType = Formula.Type.valueOf(request.getParameter("type"));
     formula.setFormulaType(formulaType);

trunk/www/views/formulas/list_formulas.jsp

@@ -59 +59 @@
   private static final Enumeration<String, String> types = new Enumeration<String, String>();
   private static final Enumeration<String, String> parsers = new Enumeration<String, String>();
+  private static final Enumeration<String, String> avgMethods = new Enumeration<String, String>();
   private static final Enumeration<String, String> rawEnumeration = new Enumeration<String, String>();
   static
@@ -69 +70 @@
     {
       parsers.add(Integer.toString(p.getValue()), HTML.encodeTags(p.toString()));
+    }
+    for (Formula.AverageMethod m : Formula.AverageMethod.values())
+    {
+      avgMethods.add(Integer.toString(m.getValue()), HTML.encodeTags(m.toString()));
     }
     for (RawDataType rdt : RawDataTypes.getRawDataTypes())
@@ -245 +250 @@
         enumeration="<%=parsers%>"
         title="Parser"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
+        id="averageMethod"
+        property="averageMethod"
+        datatype="int"
+        enumeration="<%=avgMethods%>"
+        title="Avg. method"
         sortable="true" 
         filterable="true"
@@ -511 +526 @@
                 <tbl:cell column="type"><%=item.getFormulaType().toString()%></tbl:cell>
                 <tbl:cell column="parser"><%=item.getParser().toString()%></tbl:cell>
+                <tbl:cell column="averageMethod"><%=item.getAverageMethod().toString()%></tbl:cell>
                 <tbl:cell column="rawDataType"><%=rawDataType == null ? "<i>- none -</i>" : HTML.encodeTags(rawDataType.getName())%></tbl:cell>
                 <tbl:cell column="channels"><%=item.getChannels()%></tbl:cell>

trunk/www/views/formulas/view_formula.jsp

@@ -242 +242 @@
           %>
         </td>
+      </tr>
+      <tr>
+        <td class="prompt">Avg. method</td>
+        <td><%=formula.getAverageMethod().toString()%></td>
       </tr>
       <tr>