Changeset 550 for branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp

Timestamp:

Jan 23, 2008, 3:21:52 PM (13 years ago)

Author:

mbayer

Message:

have restructured the code completely that writes the hybs section

File:

• branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp (modified) (12 diffs)

branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp

@@ -15 +15 @@
   final String ID = sc.getId();
   final String requestId = request.getParameter("requestId");
-
 %>
 
@@ -73 +72 @@
       tissueList += frm.elements[i].value + '\t';
     }
+    if(id.match("dyeInput"))
+    {
+      dyeList += frm.elements[i].value + '\t';
+    }
     if(id.match("combinationInput"))
     {
@@ -81 +84 @@
   frm.subjectList.value = subjectList;
   frm.tissueList.value = tissueList;
+  frm.dyeList.value = dyeList;
   frm.combinationList.value = combinationList;
 }
@@ -101 +105 @@
 <input type="hidden" id="subjectList" name="subjectList" value""/>
 <input type="hidden" id="tissueList" name="tissueList" value""/>
+<input type="hidden" id="dyeList" name="dyeList" value""/>
 <input type="hidden" id="combinationList" name="combinationList" value""/>
 
@@ -120 +125 @@
     //extract the possible values from between the parentheses
     String allValues = rawFactors[i].substring(rawFactors[i].indexOf("(") + 1,
-        rawFactors[i].indexOf(")"));
+    rawFactors[i].indexOf(")"));
     String[] values = allValues.split(",");
     factorValues[i] = values;
@@ -171 +176 @@
   {
     singleChannel = true;
-  } 
+  }
   int numReplicates = Integer.parseInt(inputDataBean.getNumReplicates());
   int numTreatmentGroups = Integer.parseInt(inputDataBean.getNumTreatmentGroups());
   int numTissues = inputDataBean.getTissues().split("\n").length;
-  int numHybs = Tab2MageWriter.calcNumHybs(singleChannel,numReplicates, numTreatmentGroups, numTissues);
+  boolean dyeSwapBool = false;
+  boolean poolingBool = false;
+  if(inputDataBean.getDyeSwap().equals("yes"))
+  {
+    dyeSwapBool = true;
+  }
+  if(inputDataBean.getPooling().equals("yes"))
+  {
+    poolingBool = true;
+  }
+    
+  int numHybs = Tab2MageUtils.calcNumHybs(dyeSwapBool,poolingBool,Integer.parseInt(inputDataBean.getNumDesigns()), numReplicates, numTreatmentGroups,numTissues);
+
   System.out.println("numHybs = " + numHybs);
   System.out.println("products.length = " + products.length);
 %>
 
-<h1>Tab2MAGE Import Wizard -- File Mappings</h1>
+<h2>Tab2MAGE Import Wizard -- File Mappings</h2>
 <p>
 
@@ -198 +215 @@
     <td class="header"><h3>Subject</h3></td>
     <td class="header"><h3>Tissue</h3></td>
+    <td class="header"><h3>Dye</h3></td>
     <td class="header"><h3>Factor Value Combination</h3></td>
 
@@ -205 +223 @@
 
   <%
-    for (int i = 0; i < numHybs; i++)
-    {
+      for (int i = 0; i < numHybs; i++)
+      {
   %>
 
@@ -215 +233 @@
     <td class="input" ><select id="fileInput<%=i %>">
       <%
-          for (int k = 0; k < fileNamesArr.length; k++)
-          {
+            for (int k = 0; k < fileNamesArr.length; k++)
+            {
       %>
 
@@ -230 +248 @@
     <td class="input" ><select id="subjectInput<%=i %>">
       <%
-          for (int k = 0; k < subjectNames.length; k++)
-          {
+            for (int k = 0; k < subjectNames.length; k++)
+            {
       %>
 
@@ -245 +263 @@
     <td class="input" ><select id="tissueInput<%=i %>">
       <%
-          for (int k = 0; k < tissueNames.length; k++)
-          {
+            for (int k = 0; k < tissueNames.length; k++)
+            {
       %>
 
@@ -256 +274 @@
     </select></td>
 
-<!-- need a single cell with a select box that lets the user select from a list of unique factor value combinations -->
+    <!-- select your dye here-->
+
+    <td class="input"><select id="dyeInput<%=i %>">
+      <%
+            if (!singleChannel)
+            {
+      %>
+      <option>Cy3</option>
+      <option>Cy5</option>
+      <%
+            }
+            else
+            {
+      %>
+      <option>biotin</option>
+      <%
+      }
+      %>
+
+    </select></td>
+
+    <!-- need a single cell with a select box that lets the user select from a list of unique factor value combinations -->
 
     <td>
     <select id="combinationInput<%=i %>">
       <%
-          for (int k = 0; k < products.length; k++)
+            for (int k = 0; k < products.length; k++)
+            {
+          //make a String with all the factor values in this combination
+          //separate values in each combi with a space
+          String combi = "";
+          for (int j = 0; j < products[k].length; j++)
           {
-            //make a String with all the factor values in this combination
-            //separate values in each combi with a space
-            String combi = "";
-            for (int j = 0; j < products[k].length; j++)
-            {
-              combi += products[k][j] + " ";
-            }
+            combi += products[k][j] + " ";
+          }
       %>