Changeset 3904

Timestamp:

Oct 20, 2010, 4:47:19 PM (13 years ago)

Author:

olle

Message:

Refs #700. Refs #287. First version of support for simple search form
for X!Tandem searches:

1. Class/file action/xTandemInput/ViewActiveXTandemParameterSetStorage.java

in client/servlet/ updated to support both a simple and an advanced X!Tandem search form:

1. New public static valid parameter VBoolean VXTANDEMPARAMETERSETSIMPLEFORMFLAG

added. It is used to store a flag indicating if a simple form is desired.

2. Public method void runMe() updated to retrieve the value of new valid

parameter VBoolean VXTANDEMPARAMETERSETSIMPLEFORMFLAG and set a flag variable useSimpleForm indicating if a simple form is desired. If the value of the valid parameter is null, the latter variable is set to true, as a simple form is the default. Since the value of the new valid parameter only is null the first time the action is entered for the form, the value is also used to set a boolean flag variable firstEntry. If a simple form is to be used, form class XTandemParameterSetFormSimple is used,
otherwise class XTandemParameterSetForm.
The first time the action is entered for a form X!Tandem data is read
from the database, otherwise it is retrieved from data supplied with the form. In this case, one of two new methods named updateAdvancedFormMultipleChoiceFields(...)
is called to update the multiple choice data in the current form.
A new button is added to toggle the form type between simple and advanced. This button sets the value of valid parameter VXTANDEMPARAMETERSETSIMPLEFORMFLAG to force a change of form type when the action is re-entered.

3. New private method

XTandemParameterSetForm updateAdvancedFormMultipleChoiceFields(XTandemParameterSetForm form)
added. It updates advanced form multiple choice fields.

4. New private method

XTandemParameterSetFormSimple updateAdvancedFormMultipleChoiceFields(XTandemParameterSetFormSimple form)
added. It updates simple form multiple choice fields.

5. New private convenience method

List<String> fetchValidStringList(String quantityName, VString param)
added. It fetches a string list from for a VString valid parameter from the HTTP request.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

Location:

trunk/client/servlet/src

Files:

• locale/en/dictionary (modified) (2 diffs)
• org/proteios/action/xTandemInput/ViewActiveXTandemParameterSetStorage.java (modified) (7 diffs)

trunk/client/servlet/src/locale/en/dictionary

@@ -51 +51 @@
 Address=Address
 Administrator=Administrator
+AdvancedSearchForm=Advanced Search Form
 All=All
 AllowedFDR=Allowed FDR
@@ -770 +771 @@
 Show=Show
 SignalToNoiseRatio=S/N
+SimpleSearchForm=Simple Search Form
 SizeInBytes=Size (bytes)
 Size=Size

trunk/client/servlet/src/org/proteios/action/xTandemInput/ViewActiveXTandemParameterSetStorage.java

@@ -42 +42 @@
 import org.proteios.io.XTandemParameterFileUtil;
 import org.proteios.io.XTandemParameterSet;
-//import org.proteios.io.XTandemParameterSetOptionsUtil;
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
+import se.lu.thep.waf.constraints.VBoolean;
 import se.lu.thep.waf.constraints.VInteger;
+import se.lu.thep.waf.constraints.VString;
 
 /**
@@ -55 +56 @@
   public static final VInteger VXTANDEMPARAMETERSETSTORAGEID = new VInteger(
     "active.xtandemparametersetstorage.id", 1, false);
+  public static final VBoolean VXTANDEMPARAMETERSETSIMPLEFORMFLAG = new VBoolean(
+    "active.xtandemparametersetstoragesimpleformflag", false);
 
 
@@ -85 +88 @@
     List<Integer> spectrumFileIds = getValidIntegerList(SearchXTandem.VSPECTRUMFILEID);
     log.debug("spectrumFileIds = " + spectrumFileIds);
+    // Get the useSimpleForm flag
+    Boolean useSimpleForm = getValidBoolean(VXTANDEMPARAMETERSETSIMPLEFORMFLAG);
+    log.debug("useSimpleForm from VXTANDEMPARAMETERSETSIMPLEFORMFLAG = " + useSimpleForm);
+    boolean firstEntry = false;
+    if (useSimpleForm == null)
+    {
+      // Default form type is simple form
+      useSimpleForm = true;
+      firstEntry = true;
+    }
+    log.debug("useSimpleForm = " + useSimpleForm);
+    log.debug("firstEntry = " + firstEntry);
     //
     DbControl dc = newDbControl();
@@ -94 +109 @@
     xTandemParameterFileUtil.setXMLInputStream(iStream);
     XTandemParameterSet xTandemParameterSet = xTandemParameterFileUtil.fetchXTandemParameterSet();
-    Form xTandemParameterSetForm = new XTandemParameterSetForm(xTandemParameterSet);
+    // Get X!Tandem parameter set display form
+    Form xTandemParameterSetDisplayForm;
+    if (useSimpleForm)
+    {
+      log.debug("### Simple X!Tandem Parameter Set Form");
+      // Use simple X!Tandem parameter set form
+      if (firstEntry)
+      {
+        // Fill in form fields with data from stored X!Tandem parameter set
+        Form xTandemParameterSetFormSimple = new XTandemParameterSetFormSimple(xTandemParameterSet);
+        xTandemParameterSetDisplayForm = xTandemParameterSetFormSimple;
+      }
+      else
+      {
+        // Fill in form fields with data from previously displayed simple/advanced form
+        Form xTandemParameterSetFormSimple = new XTandemParameterSetFormSimple();
+        populateForm(xTandemParameterSetFormSimple);
+        xTandemParameterSetFormSimple = updateSimpleFormMultipleChoiceFields((XTandemParameterSetFormSimple) xTandemParameterSetFormSimple);
+        xTandemParameterSetDisplayForm = xTandemParameterSetFormSimple;
+      }
+    }
+    else
+    {
+      log.debug("### Advanced X!Tandem Parameter Set Form");
+      // Use advanced X!Tandem parameter set form
+      if (firstEntry)
+      {
+        // Fill in form fields with data from stored X!Tandem parameter set       
+        Form xTandemParameterSetForm = new XTandemParameterSetForm(xTandemParameterSet);
+        xTandemParameterSetDisplayForm = xTandemParameterSetForm;
+      }
+      else
+      {
+        // Fill in form fields with data from previously displayed simple/advanced form
+        Form xTandemParameterSetForm = new XTandemParameterSetForm();
+        populateForm(xTandemParameterSetForm);
+        xTandemParameterSetForm = updateAdvancedFormMultipleChoiceFields((XTandemParameterSetForm) xTandemParameterSetForm);
+        xTandemParameterSetDisplayForm = xTandemParameterSetForm;
+      }
+    }
     /***********************************************************************
      * Annotations table
@@ -139 +193 @@
       for (Integer spectrumFileId : spectrumFileIds)
       {
-        getFormFactory().addHiddenField(xTandemParameterSetForm, SearchXTandem.VSPECTRUMFILEID, spectrumFileId);
+        getFormFactory().addHiddenField(xTandemParameterSetDisplayForm, SearchXTandem.VSPECTRUMFILEID, spectrumFileId);
       }
       searchXTandemViaWebInterface.addParameter(SearchXTandem.VXTANDEMUSEWEBINTERFACEFLAG, true);
@@ -169 +223 @@
       */
     }
-    xTandemParameterSetForm.setToolbar(toolbar);
+    // Add button to toggle between simple/advanced form
+    String toggleFormTypeButtonLabel;
+    if (useSimpleForm)
+    {
+      toggleFormTypeButtonLabel = new String("AdvancedSearchForm");
+    }
+    else
+    {
+      toggleFormTypeButtonLabel = new String("SimpleSearchForm");
+    }
+    ActionLink toggleFormTypeButton = getActionLink(ViewActiveXTandemParameterSetStorage.class, toggleFormTypeButtonLabel);
+    toggleFormTypeButton.addParameter(VXTANDEMPARAMETERSETSIMPLEFORMFLAG, !useSimpleForm);
+    toggleFormTypeButton.addParameter(VXTANDEMPARAMETERSETSTORAGEID, xtpssId);
+    toolbar.add(toggleFormTypeButton);
+    // Add tool bar
+    xTandemParameterSetDisplayForm.setToolbar(toolbar);
     /***********************************************************************
      * Layout
@@ -183 +252 @@
     ts.add(annotations);
     */
-    layout.add(xTandemParameterSetForm);
+    layout.add(xTandemParameterSetDisplayForm);
     setLayout(layout);
   }
+
+
+  /**
+   * Update advanced form multiple choice fields.
+   * 
+   * @param form XTandemParameterSetForm An advanced X!Tandem parameter set form.
+   * @return XTandemParameterSetForm The updated form.
+   */
+  private XTandemParameterSetForm updateAdvancedFormMultipleChoiceFields(XTandemParameterSetForm form)
+  {
+    List<String> stringList;
+    // Residue potential modification mass
+    stringList = fetchValidStringList("residue potential modification mass",
+      XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT);
+    if (stringList != null)
+    {
+      form.residuePotentialModificationMassSB.selectOptions(stringList);
+    }
+    // Protein taxon Eukaryotes
+    stringList = fetchValidStringList("protein taxon Eukaryotes",
+      XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON);
+    if (stringList != null)
+    {
+      form.taxonSB.selectOptions(stringList);
+    }
+    // Protein taxon Prokaryotes
+    stringList = fetchValidStringList("protein taxon Prokaryotes",
+      XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON1);
+    if (stringList != null)
+    {
+      form.taxon1SB.selectOptions(stringList);
+    }
+    // Refine potential modification mass
+    List<Option> startList = form.refinePotentialModificationMassSB.getOptions();
+    if (startList != null)
+    {
+      log.debug("Start - refine potential modification mass select list size: " + startList.size());      
+      for (Option opt: startList)
+      {
+        if (opt.isSelected())
+        {
+          log.debug("Start - refine potential modification mass selected: \"" + opt.getValue() + "\" content: \"" + opt.getValue() + "\"");
+        }
+      }
+    }
+    stringList = fetchValidStringList("refine potential modification mass",
+      XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
+    log.debug("refine potential modification mass select list = " + stringList);
+    if (stringList != null)
+    {
+      log.debug("refine potential modification mass select field list size = " + stringList.size());
+      form.refinePotentialModificationMassSB.selectOptions(stringList);
+    }
+    return form;
+  }
+
+
+  /**
+   * Update simple form multiple choice fields.
+   * 
+   * @param form XTandemParameterSetFormSimple A simple X!Tandem parameter set form.
+   * @return XTandemParameterSetFormSimple The updated form.
+   */
+  private XTandemParameterSetFormSimple updateSimpleFormMultipleChoiceFields(XTandemParameterSetFormSimple form)
+  {
+    List<String> stringList;
+    // Residue potential modification mass
+    stringList = fetchValidStringList("residue potential modification mass",
+      XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT);
+    if (stringList != null)
+    {
+      form.residuePotentialModificationMassSB.selectOptions(stringList);
+    }
+    // Protein taxon Eukaryotes
+    stringList = fetchValidStringList("protein taxon Eukaryotes",
+      XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON);
+    if (stringList != null)
+    {
+      form.taxonSB.selectOptions(stringList);
+    }
+    // Protein taxon Prokaryotes
+    stringList = fetchValidStringList("protein taxon Prokaryotes",
+      XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON1);
+    if (stringList != null)
+    {
+      form.taxon1SB.selectOptions(stringList);
+    }
+    // Refine potential modification mass
+    stringList = fetchValidStringList("refine potential modification mass",
+      XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
+    log.debug("refine potential modification mass select list = " + stringList);
+    if (stringList != null)
+    {
+      form.refinePotentialModificationMassSB.selectOptions(stringList);
+    }
+    return form;
+  }
+
+
+  /**
+   * Convenience method for fetching string list from request.
+   * 
+   * @param quantityName String Name of the list quantity.
+   * @param param VString Valid parameter coupled to the list.
+   * @return List<String> The string list obtained from the request.
+   */
+  private List<String> fetchValidStringList(String quantityName, VString param)
+  {
+    // Fetch string list from request
+    List<String> stringList = null;
+    try
+    {
+      stringList = getValidStringList(param);
+      log.debug(quantityName + " = " + stringList);
+    }
+    catch (InvalidParameterValue e)
+    {
+      log.debug("InvalidParameterValue when trying to obtain " + quantityName);
+    }
+    return stringList;
+  }
 }