Changeset 3881

Timestamp:

Oct 13, 2010, 9:05:49 AM (13 years ago)

Author:

olle

Message:

Refs #700. Refs #698. X!Tandem parameter set form now created by its
own class:

1. New class/file gui/form/XTandemParameterSetForm.java in client/servlet/

added:

1. Valid parameters related to the X!Tandem parameter set fields were

moved to the new class from class/file
action/xTandemInput/SaveXTandemParameterSetStorage.java in client/servlet/.

2. Two constructors were created, one default constructor without

arguments that creates all fields in the form, and a constructor with an
XTandemParameterSet instance as argument, which calls the default constructor
and then sets field values to the ones in the given XTandemParameterSet
instance.

3. Management of option alternatives were moved to two new methods,

fetchDefaultOptionAlternatives() for setting default options, and
fetchOptionAlternatives(), that exchanges the former for option alternatives
obtained from an GPM web site, if avaliable.

2. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java in

client/servlet updated:

1. Valid parameters related to the X!Tandem parameter set fields were

moved to the new XTandemParameterSetForm class.

2. X!Tandem parameter set values are transfered to the current form by

creating a temporary X!Tandem parameter set form with up-to-date values,
after which the fields in the latter are added as hidden fields by
new private method
Form addFormFields(Form targetForm, Form sourceForm)

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

in client/servlet/ updated:

1. Public method void runMe() updated by creating X!Tandem parameter set

form by new class XTandemParameterSetForm.

2. Old methods related to creation of an X!Tandem parameter set form

and adding X!Tandem parameter set fields to a fieldset have been removed:
private List<Option> stringListToOptionList(List<String> stringList)
public Form getXTandemParameterSetForm(...)
public Fieldset addXTandemParameterSetToFieldset(...)
public Fieldset addXTandemParameterSetListPathFieldsToFieldset(...)
public Fieldset addXTandemParameterSetSpectrumFieldsToFieldset(...)
public Fieldset addXTandemParameterSetResidueFieldsToFieldset(...)
public Fieldset addXTandemParameterSetProteinFieldsToFieldset(...)
public Fieldset addXTandemParameterSetRefineFieldsToFieldset(...)
public Fieldset addXTandemParameterSetScoringFieldsToFieldset(...)
public Fieldset addXTandemParameterSetOutputFieldsToFieldset(...)
private boolean itemInOptionList(List<Option> optionList, String item)
private boolean allItemsInOptionList(List<Option> optionList, List<String> itemList)
private List<String> listStringToStringList(String listString, String delimiterRegex)

4. Class/file gui/form/Select.java in client/servlet/ updated:
5. Public constructor Select(D param, List<Option> optionList, List<String> selected)

updated by first checking if selected list is null before using it.

2. New public method void selectOptions(List<String> selected) added.

It sets all options matching any value in the input list to selected.

Location:

trunk/client/servlet/src/org/proteios

Files:

• action/xTandemInput/SaveXTandemParameterSetStorage.java (modified) (16 diffs)
• action/xTandemInput/ViewActiveXTandemParameterSetStorage.java (modified) (5 diffs)
• gui/form/Select.java (modified) (2 diffs)
• gui/form/XTandemParameterSetForm.java (added)

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

@@ -48 +48 @@
 import org.proteios.core.query.Hql;
 import org.proteios.core.query.Restrictions;
+import org.proteios.gui.GUIElement;
 import org.proteios.gui.Title;
 import org.proteios.gui.Toolbar;
@@ -57 +58 @@
 import se.lu.thep.waf.constraints.InvalidParameterValue;
 import se.lu.thep.waf.constraints.VInteger;
+import se.lu.thep.waf.constraints.VParameter;
 import se.lu.thep.waf.constraints.VString;
 
@@ -67 +69 @@
   public static final VInteger VXTANDEMPARAMETERFILEID = new VInteger(
     "xTandemParameterFileId", 0, false);
-  public static final VString VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS = new VString("XTandemListPathDefaultParameters", 0,
-    255, false);
-  public static final VString VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION = new VString("XTandemListPathTaxonomyInformation", 0,
-    255, false);
-  public static final VString VXTANDEM_SPECTRUM_PATH = new VString("XTandemSpectrumPath", 0,
-    255, false);
-  public static final VString VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR = new VString("XTandemSpectrumFragmentMonoisotopicMassError", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS = new VString("XTandemSpectrumParentMonoisotopicMassErrorPlus", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS = new VString("XTandemSpectrumParentMonoisotopicMassErrorMinus", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR = new VString("XTandemSpectrumParentMonoisotopicMassIsotopeError", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS = new VString("XTandemSpectrumFragmentMonoisotopicMassErrorUnits", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS = new VString("XTandemSpectrumParentMonoisotopicMassErrorUnits", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_FRAG_MASS_TYPE = new VString("XTandemSpectrumFragmentMassType", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_DYNAMIC_RANGE = new VString("XTandemSpectrumDynamicRange", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_TOTAL_PEAKS = new VString("XTandemSpectrumTotalPeaks", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE = new VString("XTandemSpectrumMaximumParentCharge", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION = new VString("XTandemSpectrumUseNoiseSuppression", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H = new VString("XTandemSpectrumMinimumParentMPlusH", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H = new VString("XTandemSpectrumMaximumParentMPlusH", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_MIN_FRAG_MZ = new VString("XTandemSpectrumMinimumFragmentMz", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_MIN_PEAKS = new VString("XTandemSpectrumMinimumPeaks", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_THREADS = new VString("XTandemSpectrumThreads", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE = new VString("XTandemSpectrumSequenceBatchSize", 0,
-    32, false);
-  public static final VString VXTANDEM_SPECTRUM_USE_CONDITIONING = new VString("XTandemSpectrumUseConditioning", 0,
-    32, false);
-  public static final VString VXTANDEM_RESIDUE_MODIFICATION_MASS_SELECT = new VString("XTandemResidueModificationMassSelect", 0,
-    32, false);
-  public static final VString VXTANDEM_RESIDUE_MODIFICATION_MASS = new VString("XTandemResidueModificationMass", 0,
-    150, false);
-  public static final VString VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT = new VString("XTandemResiduePotentialModificationMassSelect", 0,
-    32, false);
-  public static final VString VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS = new VString("XTandemResiduePotentialModificationMass", 0,
-    150, false);
-  public static final VString VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF = new VString("XTandemResiduePotentialModificationMotif", 0,
-    100, false);
-  public static final VString VXTANDEM_PROTEIN_TAXON = new VString("XTandemProteinTaxon", 0,
-    64, false);
-  public static final VString VXTANDEM_PROTEIN_TAXON1 = new VString("XTandemProteinTaxon1", 0,
-    64, false);
-  public static final VString VXTANDEM_PROTEIN_CLEAVAGE_SITE_SELECT = new VString("XTandemProteinCleavageSiteSelect", 0,
-    32, false);
-  public static final VString VXTANDEM_PROTEIN_CLEAVAGE_SITE = new VString("XTandemProteinCleavageSite", 0,
-    32, false);
-  public static final VString VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE = new VString("XTandemProteinModifiedResidueMassFile", 0,
-    32, false);
-  public static final VString VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE = new VString("XTandemProteinCleavageNTerminalMassChange", 0,
-    32, false);
-  public static final VString VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE = new VString("XTandemProteinCleavageCTerminalMassChange", 0,
-    32, false);
-  public static final VString VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS = new VString("XTandemProteinNTerminalResidueModificationMass", 0,
-    32, false);
-  public static final VString VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS = new VString("XTandemProteinCTerminalResidueModificationMass", 0,
-    32, false);
-  public static final VString VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT = new VString("XTandemProteinHomologManagement", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE = new VString("XTandemRefine", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_MODIFICATION_MASS = new VString("XTandemRefineModificationMass", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_SEQUENCE_PATH = new VString("XTandemRefineSequencePath", 0,
-    255, false);
-  public static final VString VXTANDEM_REFINE_TIC_PERCENT = new VString("XTandemRefineTicPercent", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_SPECTRUM_SYNTHESIS = new VString("XTandemRefineSpectrumSynthesis", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE = new VString("XTandemRefineMaximumValidExpectationValue", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS = new VString("XTandemRefinePotentialNTerminusModifications", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS = new VString("XTandemRefinePotentialCTerminusModifications", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE = new VString("XTandemRefineUnanticipatedCleavage", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT = new VString("XTandemRefinePotentialModificationMassSelect", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS = new VString("XTandemRefinePotentialModificationMass", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_POINT_MUTATIONS = new VString("XTandemRefinePointMutations", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT = new VString("XTandemRefineUsePotentialModificationsForFullRefinement", 0,
-    32, false);
-  public static final VString VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF = new VString("XTandemRefinePotentialModificationMotif", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_MIN_ION_COUNT = new VString("XTandemScoringMinIonCount", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES = new VString("XTandemScoringMaxMissedCleavageSites", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_X_IONS = new VString("XTandemScoringXIons", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_Y_IONS = new VString("XTandemScoringYIons", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_Z_IONS = new VString("XTandemScoringZIons", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_A_IONS = new VString("XTandemScoringAIons", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_B_IONS = new VString("XTandemScoringBIons", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_C_IONS = new VString("XTandemScoringCIons", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_CYCLIC_PERMUTATION = new VString("XTandemScoringCyclicPermutation", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_INCLUDE_REVERSE = new VString("XTandemScoringIncludeReverse", 0,
-    32, false);
-  public static final VString VXTANDEM_SCORING_ALGORITHM = new VString("XTandemScoringAlgorithm", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_PATH = new VString("XTandemOutputPath", 0,
-    255, false);
-  public static final VString VXTANDEM_OUTPUT_LOG_PATH = new VString("XTandemOutputLogPath", 0,
-    255, false);
-  public static final VString VXTANDEM_OUTPUT_MESSAGE = new VString("XTandemOutputMessage", 0,
-    255, false);
-  public static final VString VXTANDEM_OUTPUT_SEQUENCE_PATH = new VString("XTandemOutputSequencePath", 0,
-    255, false);
-  public static final VString VXTANDEM_OUTPUT_SORT_RESULTS_BY = new VString("XTandemOutputSortResultsBy", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_PATH_HASHING = new VString("XTandemOutputPathHashing", 0,
-    255, false);
-  public static final VString VXTANDEM_OUTPUT_XSL_PATH = new VString("XTandemOutputXslPath", 0,
-    255, false);
-  public static final VString VXTANDEM_OUTPUT_PARAMETERS = new VString("XTandemOutputParameters", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_PERFORMANCE = new VString("XTandemOutputPerformance", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_SPECTRA = new VString("XTandemOutputSpectra", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_HISTOGRAMS = new VString("XTandemOutputHistograms", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_PROTEINS = new VString("XTandemOutputProteins", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_SEQUENCES = new VString("XTandemOutputSequences", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY = new VString("XTandemOutputOneSequenceCopy", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_RESULTS = new VString("XTandemOutputResults", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE = new VString("XTandemOutputMaximumValidExpectationValue", 0,
-    32, false);
-  public static final VString VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH = new VString("XTandemOutputHistogramColumnWidth", 0,
-    32, false);
 
   @Override
@@ -291 +137 @@
         // XTandemParameterSetStorage form
         Form form = new SaveAsXTandemStorageForm(xtpss, xTandemParameterSet);
+        // Hidden fields for transferring values of XTandem parameter set
+        Form xTandemParameterSetForm = new XTandemParameterSetForm();
+        populateForm(xTandemParameterSetForm);
+        form = addFormFields(form, xTandemParameterSetForm);
         // Toolbar
         Toolbar tb = new Toolbar();
@@ -505 +355 @@
 
   /**
+   * Adds form fields in source form as hidden fields to target form.
+   * @param targetForm Form The form to add hidden fields to.
+   * @param sourceForm Form The form to take fields from.
+   * @return Form The updated target form.
+   */
+  private Form addFormFields(Form targetForm, Form sourceForm)
+  {
+    // Get last target fieldset to add hidden fields to
+    Fieldset targetFS = null;
+    for (Fieldset fieldset: targetForm.getFieldsets())
+    {
+      targetFS = fieldset;
+    }
+    if (targetFS == null)
+    {
+      log.debug("No fieldset in form " + targetForm.getTitle() + " to add hidden fields to");
+      // Create new fieldset without title to store hidden fields
+      targetFS = new Fieldset();
+      targetForm.addFieldset(targetFS);
+    }
+    else
+    {
+      log.debug("Fields from form " + sourceForm.getTitle() + " added as hidden fields to fieldset " + targetFS.getTitle() + " in form " + targetForm.getTitle());
+    }
+    for (Fieldset sourceFS: sourceForm.getFieldsets())
+    {
+      for (GUIElement guiElement: sourceFS.getFields())
+      {
+         if (guiElement instanceof Select)
+           {
+           Select sourceS = ((Select) guiElement);
+           TextField field = new TextField(sourceS.getParam());
+           field.setId(sourceS.getId());
+           field.setLabel(sourceS.getLabel());
+           try
+           {
+             List<String> stringList = getValidStringList((VString) sourceS.getParam());
+             log.debug("Source select - " + sourceS.getLabel() + " string list = " + stringList);
+             String delimiterString = new String(",");
+             if (sourceS.getLabel().equals("XTandemProteinTaxonEukaryotes") ||
+                 sourceS.getLabel().equals("XTandemProteinTaxonProkaryotes"))
+             {
+               delimiterString = new String(", ");
+             }
+             String listString = stringListToListString(stringList, delimiterString);
+             field.setValue(listString);
+           }
+           catch(InvalidParameterValue e)
+           {
+             log.debug("Source select - " + sourceS.getLabel() + " InvalidParameterValue: " + e);
+           }
+           log.debug("Target field - " + field.getLabel() + ": " + field.getValue());
+           field.setHidden(true);
+           targetFS.add(field);
+           }
+         else if (guiElement instanceof TextField)
+           {
+           TextField sourceF = ((TextField) guiElement);
+           TextField field = new TextField(sourceF.getParam());
+           field.setId(sourceF.getId());
+           field.setLabel(sourceF.getLabel());
+           field.setValue(sourceF.getValue());
+           field.setHidden(true);
+           targetFS.add(field);
+           }
+      }
+    }
+    return targetForm;
+  }
+
+
+  /**
    * Fetches values of XTandemParameterSet variables from valid parameters
    * and stores them in corresponding variables in an XTandemParameterSet
@@ -519 +441 @@
     XTandemParameterSet xTandemParameterSet = new XTandemParameterSet();
     //
-    String listPathDefaultParameters = getString(VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS);
+    String listPathDefaultParameters = getString(XTandemParameterSetForm.VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS);
     xTandemParameterSet.setListPathDefaultParameters(listPathDefaultParameters);
     log.debug("listPathDefaultParameters = " + listPathDefaultParameters);
     //
-    String listPathTaxonomyInformation = getString(VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION);
+    String listPathTaxonomyInformation = getString(XTandemParameterSetForm.VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION);
     xTandemParameterSet.setListPathTaxonomyInformation(listPathTaxonomyInformation);
     log.debug("listPathTaxonomyInformation = " + listPathTaxonomyInformation);
     //
-    String spectrumPath = getString(VXTANDEM_SPECTRUM_PATH);
+    String spectrumPath = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PATH);
     xTandemParameterSet.setSpectrumPath(spectrumPath);
     log.debug("spectrumPath = " + spectrumPath);
     //
-    String spectrumFragMiMassError = getString(VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR);
+    String spectrumFragMiMassError = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR);
     xTandemParameterSet.setSpectrumFragmentMonoisotopicMassError(spectrumFragMiMassError);
     log.debug("spectrumFragMiMassError = " + spectrumFragMiMassError);
     //
-    String spectrumParentMiMassErrorPlus = getString(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS);
+    String spectrumParentMiMassErrorPlus = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS);
     xTandemParameterSet.setSpectrumParentMonoisotopicMassErrorPlus(spectrumParentMiMassErrorPlus);
     log.debug("spectrumParentMiMassErrorPlus = " + spectrumParentMiMassErrorPlus);
     //
-    String spectrumParentMiMassErrorMinus = getString(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS);
+    String spectrumParentMiMassErrorMinus = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS);
     xTandemParameterSet.setSpectrumParentMonoisotopicMassErrorMinus(spectrumParentMiMassErrorMinus);
     log.debug("spectrumParentMiMassErrorMinus = " + spectrumParentMiMassErrorMinus);
     //
-    String spectrumParentMiMassIsotopeError = getString(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR);
+    String spectrumParentMiMassIsotopeError = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR);
     xTandemParameterSet.setSpectrumParentMonoisotopicMassIsotopeError(spectrumParentMiMassIsotopeError);
     log.debug("spectrumParentMiMassIsotopeError = " + spectrumParentMiMassIsotopeError);
     //
-    String spectrumFragMiMassErrorUnits = getString(VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS);
+    String spectrumFragMiMassErrorUnits = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS);
     xTandemParameterSet.setSpectrumFragmentMonoisotopicMassErrorUnits(spectrumFragMiMassErrorUnits);
     log.debug("spectrumFragMiMassErrorUnits = " + spectrumFragMiMassErrorUnits);
     //
-    String spectrumParentMiMassErrorUnits = getString(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS);
+    String spectrumParentMiMassErrorUnits = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS);
     xTandemParameterSet.setSpectrumParentMonoisotopicMassErrorUnits(spectrumParentMiMassErrorUnits);
     log.debug("spectrumParentMiMassErrorUnits = " + spectrumParentMiMassErrorUnits);
     //
-    String spectrumFragMassType = getString(VXTANDEM_SPECTRUM_FRAG_MASS_TYPE);
+    String spectrumFragMassType = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_FRAG_MASS_TYPE);
     xTandemParameterSet.setSpectrumFragmentMassType(spectrumFragMassType);
     log.debug("spectrumFragMassType = " + spectrumFragMassType);
     //
-    String spectrumDynamicRange = getString(VXTANDEM_SPECTRUM_DYNAMIC_RANGE);
+    String spectrumDynamicRange = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_DYNAMIC_RANGE);
     xTandemParameterSet.setSpectrumDynamicRange(spectrumDynamicRange);
     log.debug("spectrumDynamicRange = " + spectrumDynamicRange);
     //
-    String spectrumTotalPeaks = getString(VXTANDEM_SPECTRUM_TOTAL_PEAKS);
+    String spectrumTotalPeaks = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_TOTAL_PEAKS);
     xTandemParameterSet.setSpectrumTotalPeaks(spectrumTotalPeaks);
     log.debug("spectrumTotalPeaks = " + spectrumTotalPeaks);
     //
-    String spectrumMaxParentCharge = getString(VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE);
+    String spectrumMaxParentCharge = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE);
     xTandemParameterSet.setSpectrumMaximumParentCharge(spectrumMaxParentCharge);
     log.debug("spectrumMaxParentCharge = " + spectrumMaxParentCharge);
     //
-    String spectrumUseNoiseSuppression = getString(VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION);
+    String spectrumUseNoiseSuppression = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION);
     xTandemParameterSet.setSpectrumUseNoiseSuppression(spectrumUseNoiseSuppression);
     log.debug("spectrumUseNoiseSuppression = " + spectrumUseNoiseSuppression);
     //
-    String spectrumMinParentMPlusH = getString(VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H);
+    String spectrumMinParentMPlusH = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H);
     xTandemParameterSet.setSpectrumMinimumParentMPlusH(spectrumMinParentMPlusH);
     log.debug("spectrumMinParentMPlusH = " + spectrumMinParentMPlusH);
     //
-    String spectrumMaxParentMPlusH = getString(VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H);
+    String spectrumMaxParentMPlusH = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H);
     xTandemParameterSet.setSpectrumMaximumParentMPlusH(spectrumMaxParentMPlusH);
     log.debug("spectrumMaxParentMPlusH = " + spectrumMaxParentMPlusH);
     //
-    String spectrumMinFragmentMz = getString(VXTANDEM_SPECTRUM_MIN_FRAG_MZ);
+    String spectrumMinFragmentMz = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MIN_FRAG_MZ);
     xTandemParameterSet.setSpectrumMinimumFragmentMz(spectrumMinFragmentMz);
     log.debug("spectrumMinFragmentMz = " + spectrumMinFragmentMz);
     //
-    String spectrumMinPeaks = getString(VXTANDEM_SPECTRUM_MIN_PEAKS);
+    String spectrumMinPeaks = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MIN_PEAKS);
     xTandemParameterSet.setSpectrumMinimumPeaks(spectrumMinPeaks);
     log.debug("spectrumMinPeaks = " + spectrumMinPeaks);
     //
-    String spectrumThreads = getString(VXTANDEM_SPECTRUM_THREADS);
+    String spectrumThreads = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_THREADS);
     xTandemParameterSet.setSpectrumThreads(spectrumThreads);
     log.debug("spectrumThreads = " + spectrumThreads);
     //
-    String spectrumSequenceBatchSize = getString(VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE);
+    String spectrumSequenceBatchSize = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE);
     xTandemParameterSet.setSpectrumSequenceBatchSize(spectrumSequenceBatchSize);
     log.debug("spectrumSequenceBatchSize = " + spectrumSequenceBatchSize);
     //
-    String spectrumUseConditioning = getString(VXTANDEM_SPECTRUM_USE_CONDITIONING);
+    String spectrumUseConditioning = getString(XTandemParameterSetForm.VXTANDEM_SPECTRUM_USE_CONDITIONING);
     xTandemParameterSet.setSpectrumUseConditioning(spectrumUseConditioning);
     log.debug("spectrumUseConditioning = " + spectrumUseConditioning);
@@ -610 +532 @@
      */
     // Residue modification mass select box
-    String residueModificationMassSelect = getString(VXTANDEM_RESIDUE_MODIFICATION_MASS_SELECT);
+    String residueModificationMassSelect = getString(XTandemParameterSetForm.VXTANDEM_RESIDUE_MODIFICATION_MASS_SELECT);
     log.debug("residueModificationMassSelect = " + residueModificationMassSelect);
     // Residue modification mass from entry field
-    String residueModificationMass = getString(VXTANDEM_RESIDUE_MODIFICATION_MASS);
+    String residueModificationMass = getString(XTandemParameterSetForm.VXTANDEM_RESIDUE_MODIFICATION_MASS);
     log.debug("residueModificationMass (own) = " + residueModificationMass);
     // If no entered value, use selected value
@@ -638 +560 @@
     // Residue potential modification mass select box list
     //String residuePotentialModificationMassSelect = getString(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT);
-    List<String> residuePotentialModificationMassSelectList = getValidStringList(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT);
+    List<String> residuePotentialModificationMassSelectList = getValidStringList(XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT);
     log.debug("residuePotentialModificationMassSelectList = " + residuePotentialModificationMassSelectList);
     residuePotentialModificationMassSelectList = uniqueStringItemList(residuePotentialModificationMassSelectList);
@@ -648 +570 @@
     log.debug("residuePotentialModificationMassSelect = \"" + residuePotentialModificationMassSelect + "\"");
     // Residue potential modification mass list from entry field
-    String residuePotentialModificationMass = getString(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS);
+    String residuePotentialModificationMass = getString(XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS);
     log.debug("residuePotentialModificationMass (own) = " + residuePotentialModificationMass);
     // If no entered values, use selected values
@@ -661 +583 @@
     log.debug("residuePotentialModificationMass = " + residuePotentialModificationMass);
     //
-    String residuePotentialModificationMotif = getString(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF);
+    String residuePotentialModificationMotif = getString(XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF);
     xTandemParameterSet.setResiduePotentialModificationMotif(residuePotentialModificationMotif);
     log.debug("residuePotentialModificationMotif = " + residuePotentialModificationMotif);
@@ -676 +598 @@
     //String proteinTaxon = getString(VXTANDEM_PROTEIN_TAXON);
     // Taxon list 1, Eukaryotes
-    List<String> proteinTaxonList = getValidStringList(VXTANDEM_PROTEIN_TAXON);
+    List<String> proteinTaxonList = getValidStringList(XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON);
     log.debug("proteinTaxonList = " + proteinTaxonList);
     proteinTaxonList = uniqueStringItemList(proteinTaxonList);
     log.debug("proteinTaxonList with unique items = " + proteinTaxonList);
     // Taxon list 2, Prokaryotes
-    List<String> proteinTaxon1List = getValidStringList(VXTANDEM_PROTEIN_TAXON1);
+    List<String> proteinTaxon1List = getValidStringList(XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON1);
     log.debug("proteinTaxon1List = " + proteinTaxon1List);
     proteinTaxon1List = uniqueStringItemList(proteinTaxon1List);
@@ -710 +632 @@
      */
     // Protein cleavage site select box
-    String proteinCleavageSiteSelect = getString(VXTANDEM_PROTEIN_CLEAVAGE_SITE_SELECT);
+    String proteinCleavageSiteSelect = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_SITE_SELECT);
     log.debug("proteinCleavageSiteSelect = " + proteinCleavageSiteSelect);
     // Protein cleavage site from entry field
-    String proteinCleavageSite = getString(VXTANDEM_PROTEIN_CLEAVAGE_SITE);
+    String proteinCleavageSite = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_SITE);
     log.debug("proteinCleavageSite (own) = " + proteinCleavageSite);
     // If no entered value, use selected value
@@ -726 +648 @@
     log.debug("proteinCleavageSite = " + proteinCleavageSite);
     //
-    String proteinModifiedResidueMassFile = getString(VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE);
+    String proteinModifiedResidueMassFile = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE);
     xTandemParameterSet.setProteinModifiedResidueMassFile(proteinModifiedResidueMassFile);
     log.debug("proteinModifiedResidueMassFile = " + proteinModifiedResidueMassFile);
     //
-    String proteinCleavageNTerminalMassChange = getString(VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE);
+    String proteinCleavageNTerminalMassChange = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE);
     xTandemParameterSet.setProteinCleavageNTerminalMassChange(proteinCleavageNTerminalMassChange);
     log.debug("proteinCleavageNTerminalMassChange = " + proteinCleavageNTerminalMassChange);
     //
-    String proteinCleavageCTerminalMassChange = getString(VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE);
+    String proteinCleavageCTerminalMassChange = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE);
     xTandemParameterSet.setProteinCleavageCTerminalMassChange(proteinCleavageCTerminalMassChange);
     log.debug("proteinCleavageCTerminalMassChange = " + proteinCleavageCTerminalMassChange);
     //
-    String proteinNTerminalResidueModificationMass = getString(VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS);
+    String proteinNTerminalResidueModificationMass = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS);
     xTandemParameterSet.setProteinNTerminalResidueModificationMass(proteinNTerminalResidueModificationMass);
     log.debug("proteinNTerminalResidueModificationMass = " + proteinNTerminalResidueModificationMass);
     //
-    String proteinCTerminalResidueModificationMass = getString(VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS);
+    String proteinCTerminalResidueModificationMass = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS);
     xTandemParameterSet.setProteinCTerminalResidueModificationMass(proteinCTerminalResidueModificationMass);
     log.debug("proteinCTerminalResidueModificationMass = " + proteinCTerminalResidueModificationMass);
     //
-    String proteinHomologManagement = getString(VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT);
+    String proteinHomologManagement = getString(XTandemParameterSetForm.VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT);
     xTandemParameterSet.setProteinHomologManagement(proteinHomologManagement);
     log.debug("proteinHomologManagement = " + proteinHomologManagement);
     //
-    String refine = getString(VXTANDEM_REFINE);
+    String refine = getString(XTandemParameterSetForm.VXTANDEM_REFINE);
     xTandemParameterSet.setRefine(refine);
     log.debug("refine = " + refine);
     //
-    String refineModificationMass = getString(VXTANDEM_REFINE_MODIFICATION_MASS);
+    String refineModificationMass = getString(XTandemParameterSetForm.VXTANDEM_REFINE_MODIFICATION_MASS);
     xTandemParameterSet.setRefineModificationMass(refineModificationMass);
     log.debug("refineModificationMass = " + refineModificationMass);
     //
-    String refineSequencePath = getString(VXTANDEM_REFINE_SEQUENCE_PATH);
+    String refineSequencePath = getString(XTandemParameterSetForm.VXTANDEM_REFINE_SEQUENCE_PATH);
     xTandemParameterSet.setRefineSequencePath(refineSequencePath);
     log.debug("refineSequencePath = " + refineSequencePath);
     //
-    String refineTicPercent = getString(VXTANDEM_REFINE_TIC_PERCENT);
+    String refineTicPercent = getString(XTandemParameterSetForm.VXTANDEM_REFINE_TIC_PERCENT);
     xTandemParameterSet.setRefineTicPercent(refineTicPercent);
     log.debug("refineTicPercent = " + refineTicPercent);
     //
-    String refineSpectrumSynthesis = getString(VXTANDEM_REFINE_SPECTRUM_SYNTHESIS);
+    String refineSpectrumSynthesis = getString(XTandemParameterSetForm.VXTANDEM_REFINE_SPECTRUM_SYNTHESIS);
     xTandemParameterSet.setRefineSpectrumSynthesis(refineSpectrumSynthesis);
     log.debug("refineSpectrumSynthesis = " + refineSpectrumSynthesis);
     //
-    String refineMaxValidExpectationValue = getString(VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE);
+    String refineMaxValidExpectationValue = getString(XTandemParameterSetForm.VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE);
     xTandemParameterSet.setRefineMaximumValidExpectationValue(refineMaxValidExpectationValue);
     log.debug("refineMaxValidExpectationValue = " + refineMaxValidExpectationValue);
     //
-    String refinePotentialNTerminusModifications = getString(VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS);
+    String refinePotentialNTerminusModifications = getString(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS);
     xTandemParameterSet.setRefinePotentialNTerminusModifications(refinePotentialNTerminusModifications);
     log.debug("refinePotentialNTerminusModifications = " + refinePotentialNTerminusModifications);
     //
-    String refinePotentialCTerminusModifications = getString(VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS);
+    String refinePotentialCTerminusModifications = getString(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS);
     xTandemParameterSet.setRefinePotentialCTerminusModifications(refinePotentialCTerminusModifications);
     log.debug("refinePotentialCTerminusModifications = " + refinePotentialCTerminusModifications);
     //
-    String refineUnanticipatedCleavage = getString(VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE);
+    String refineUnanticipatedCleavage = getString(XTandemParameterSetForm.VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE);
     xTandemParameterSet.setRefineUnanticipatedCleavage(refineUnanticipatedCleavage);
     log.debug("refineUnanticipatedCleavage = " + refineUnanticipatedCleavage);
@@ -798 +720 @@
     // Refine potential modification mass select box list
     //String refinePotentialModificationMassSelect = getString(VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
-    List<String> refinePotentialModificationMassSelectList = getValidStringList(VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
+    List<String> refinePotentialModificationMassSelectList = getValidStringList(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
     log.debug("refinePotentialModificationMassSelectList = " + refinePotentialModificationMassSelectList);
     refinePotentialModificationMassSelectList = uniqueStringItemList(refinePotentialModificationMassSelectList);
@@ -806 +728 @@
     log.debug("refinePotentialModificationMassSelect = \"" + refinePotentialModificationMassSelect + "\"");
     // Refine potential modification mass list from entry field
-    String refinePotentialModificationMass = getString(VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS);
+    String refinePotentialModificationMass = getString(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS);
     log.debug("refinePotentialModificationMass (own) = " + refinePotentialModificationMass);
     // If no entered values, use selected values
@@ -820 +742 @@
     log.debug("refinePotentialModificationMassRefine = " + refinePotentialModificationMass);
     //
-    String refinePointMutations = getString(VXTANDEM_REFINE_POINT_MUTATIONS);
+    String refinePointMutations = getString(XTandemParameterSetForm.VXTANDEM_REFINE_POINT_MUTATIONS);
     xTandemParameterSet.setRefinePointMutations(refinePointMutations);
     log.debug("refinePointMutations = " + refinePointMutations);
     //
-    String refineUsePotentialModificationsForFullRefinement = getString(VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT);
+    String refineUsePotentialModificationsForFullRefinement = getString(XTandemParameterSetForm.VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT);
     xTandemParameterSet.setRefineUsePotentialModificationsForFullRefinement(refineUsePotentialModificationsForFullRefinement);
     log.debug("refineUsePotentialModificationsForFullRefinement = " + refineUsePotentialModificationsForFullRefinement);
     //
-    String refinePotentialModificationMotifRefine = getString(VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF);
+    String refinePotentialModificationMotifRefine = getString(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF);
     xTandemParameterSet.setRefinePotentialModificationMotif(refinePotentialModificationMotifRefine);
     log.debug("refinePotentialModificationMotifRefine = " + refinePotentialModificationMotifRefine);
     //
-    String scoringMinIonCount = getString(VXTANDEM_SCORING_MIN_ION_COUNT);
+    String scoringMinIonCount = getString(XTandemParameterSetForm.VXTANDEM_SCORING_MIN_ION_COUNT);
     xTandemParameterSet.setScoringMinimumIonCount(scoringMinIonCount);
     log.debug("scoringMinIonCount = " + scoringMinIonCount);
     //
-    String scoringMaxMissedCleavageSites = getString(VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES);
+    String scoringMaxMissedCleavageSites = getString(XTandemParameterSetForm.VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES);
     xTandemParameterSet.setScoringMaximumMissedCleavageSites(scoringMaxMissedCleavageSites);
     log.debug("scoringMaxMissedCleavageSites = " + scoringMaxMissedCleavageSites);
     //
-    String scoringXIons = getString(VXTANDEM_SCORING_X_IONS);
+    String scoringXIons = getString(XTandemParameterSetForm.VXTANDEM_SCORING_X_IONS);
     xTandemParameterSet.setScoringXIons(scoringXIons);
     log.debug("scoringXIons = " + scoringXIons);
     //
-    String scoringYIons = getString(VXTANDEM_SCORING_Y_IONS);
+    String scoringYIons = getString(XTandemParameterSetForm.VXTANDEM_SCORING_Y_IONS);
     xTandemParameterSet.setScoringYIons(scoringYIons);
     log.debug("scoringYIons = " + scoringYIons);
     //
-    String scoringZIons = getString(VXTANDEM_SCORING_Z_IONS);
+    String scoringZIons = getString(XTandemParameterSetForm.VXTANDEM_SCORING_Z_IONS);
     xTandemParameterSet.setScoringZIons(scoringZIons);
     log.debug("scoringZIons = " + scoringZIons);
     //
-    String scoringAIons = getString(VXTANDEM_SCORING_A_IONS);
+    String scoringAIons = getString(XTandemParameterSetForm.VXTANDEM_SCORING_A_IONS);
     xTandemParameterSet.setScoringAIons(scoringAIons);
     log.debug("scoringAIons = " + scoringAIons);
     //
-    String scoringBIons = getString(VXTANDEM_SCORING_B_IONS);
+    String scoringBIons = getString(XTandemParameterSetForm.VXTANDEM_SCORING_B_IONS);
     xTandemParameterSet.setScoringBIons(scoringBIons);
     log.debug("scoringBIons = " + scoringBIons);
     //
-    String scoringCIons = getString(VXTANDEM_SCORING_C_IONS);
+    String scoringCIons = getString(XTandemParameterSetForm.VXTANDEM_SCORING_C_IONS);
     xTandemParameterSet.setScoringCIons(scoringCIons);
     log.debug("scoringCIons = " + scoringCIons);
     //
-    String scoringCyclicPermutation = getString(VXTANDEM_SCORING_CYCLIC_PERMUTATION);
+    String scoringCyclicPermutation = getString(XTandemParameterSetForm.VXTANDEM_SCORING_CYCLIC_PERMUTATION);
     xTandemParameterSet.setScoringCyclicPermutation(scoringCyclicPermutation);
     log.debug("scoringCyclicPermutation = " + scoringCyclicPermutation);
     //
-    String scoringIncludeReverse = getString(VXTANDEM_SCORING_INCLUDE_REVERSE);
+    String scoringIncludeReverse = getString(XTandemParameterSetForm.VXTANDEM_SCORING_INCLUDE_REVERSE);
     xTandemParameterSet.setScoringIncludeReverse(scoringIncludeReverse);
     log.debug("scoringIncludeReverse = " + scoringIncludeReverse);
     //
-    String scoringAlgorithm = getString(VXTANDEM_SCORING_ALGORITHM);
+    String scoringAlgorithm = getString(XTandemParameterSetForm.VXTANDEM_SCORING_ALGORITHM);
     xTandemParameterSet.setScoringAlgorithm(scoringAlgorithm);
     log.debug("scoringAlgorithm = " + scoringAlgorithm);
     //
-    String outputPath = getString(VXTANDEM_OUTPUT_PATH);
+    String outputPath = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_PATH);
     xTandemParameterSet.setOutputPath(outputPath);
     log.debug("outputPath = " + outputPath);
     //
-    String outputLogPath = getString(VXTANDEM_OUTPUT_LOG_PATH);
+    String outputLogPath = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_LOG_PATH);
     xTandemParameterSet.setOutputLogPath(outputLogPath);
     log.debug("outputLogPath = " + outputLogPath);
     //
-    String outputMessage = getString(VXTANDEM_OUTPUT_MESSAGE);
+    String outputMessage = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_MESSAGE);
     xTandemParameterSet.setOutputMessage(outputMessage);
     log.debug("outputMessage = " + outputMessage);
     //
-    String outputSequencePath = getString(VXTANDEM_OUTPUT_SEQUENCE_PATH);
+    String outputSequencePath = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_SEQUENCE_PATH);
     xTandemParameterSet.setOutputSequencePath(outputSequencePath);
     log.debug("outputSequencePath = " + outputSequencePath);
     //
-    String outputSortResultsBy = getString(VXTANDEM_OUTPUT_SORT_RESULTS_BY);
+    String outputSortResultsBy = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_SORT_RESULTS_BY);
     xTandemParameterSet.setOutputSortResultsBy(outputSortResultsBy);
     log.debug("outputSortResultsBy = " + outputSortResultsBy);
     //
-    String outputPathHashing = getString(VXTANDEM_OUTPUT_PATH_HASHING);
+    String outputPathHashing = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_PATH_HASHING);
     xTandemParameterSet.setOutputPathHashing(outputPathHashing);
     log.debug("outputPathHashing = " + outputPathHashing);
     //
-    String outputXslPath = getString(VXTANDEM_OUTPUT_XSL_PATH);
+    String outputXslPath = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_XSL_PATH);
     xTandemParameterSet.setOutputXslPath(outputXslPath);
     log.debug("outptuXslPath = " + outputXslPath);
     //
-    String outputParameters = getString(VXTANDEM_OUTPUT_PARAMETERS);
+    String outputParameters = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_PARAMETERS);
     xTandemParameterSet.setOutputParameters(outputParameters);
     log.debug("outputParameters = " + outputParameters);
     //
-    String outputPerformance = getString(VXTANDEM_OUTPUT_PERFORMANCE);
+    String outputPerformance = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_PERFORMANCE);
     xTandemParameterSet.setOutputPerformance(outputPerformance);
     log.debug("outputPerformance = " + outputPerformance);
     //
-    String outputSpectra = getString(VXTANDEM_OUTPUT_SPECTRA);
+    String outputSpectra = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_SPECTRA);
     xTandemParameterSet.setOutputSpectra(outputSpectra);
     log.debug("outputSpectra = " + outputSpectra);
     //
-    String outputHistograms = getString(VXTANDEM_OUTPUT_HISTOGRAMS);
+    String outputHistograms = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_HISTOGRAMS);
     xTandemParameterSet.setOutputHistograms(outputHistograms);
     log.debug("outputHistograms = " + outputHistograms);
     //
-    String outputProteins = getString(VXTANDEM_OUTPUT_PROTEINS);
+    String outputProteins = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_PROTEINS);
     xTandemParameterSet.setOutputProteins(outputProteins);
     log.debug("outputProteins = " + outputProteins);
     //
-    String outputSequences = getString(VXTANDEM_OUTPUT_SEQUENCES);
+    String outputSequences = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_SEQUENCES);
     xTandemParameterSet.setOutputSequences(outputSequences);
     log.debug("outputSequences = " + outputSequences);
     //
-    String outputOneSequenceCopy = getString(VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY);
+    String outputOneSequenceCopy = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY);
     xTandemParameterSet.setOutputOneSequenceCopy(outputOneSequenceCopy);
     log.debug("outputOneSequenceCopy = " + outputOneSequenceCopy);
     //
-    String outputResults = getString(VXTANDEM_OUTPUT_RESULTS);
+    String outputResults = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_RESULTS);
     xTandemParameterSet.setOutputResults(outputResults);
     log.debug("outputResults = " + outputResults);
     //
-    String outputMaxValidExpectationValueOutput = getString(VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE);
+    String outputMaxValidExpectationValueOutput = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE);
     xTandemParameterSet.setOutputMaximumValidExpectationValue(outputMaxValidExpectationValueOutput);
     log.debug("outputMaxValidExpectationValueOutput = " + outputMaxValidExpectationValueOutput);
     //
-    String outputHistogramColumnWidth = getString(VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH);
+    String outputHistogramColumnWidth = getString(XTandemParameterSetForm.VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH);
     xTandemParameterSet.setOutputHistogramColumnWidth(outputHistogramColumnWidth);
     log.debug("outputHistogramColumnWidth = " + outputHistogramColumnWidth);

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

@@ -30 +30 @@
 
 import java.io.InputStream;
-import java.util.ArrayList;
 import java.util.List;
 import org.proteios.ActionLink;
@@ -43 +42 @@
 import org.proteios.io.XTandemParameterFileUtil;
 import org.proteios.io.XTandemParameterSet;
-import org.proteios.io.XTandemParameterSetOptionsUtil;
+//import org.proteios.io.XTandemParameterSetOptionsUtil;
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
 import se.lu.thep.waf.constraints.VInteger;
-import se.lu.thep.waf.constraints.VString;
 
 /**
@@ -96 +94 @@
     xTandemParameterFileUtil.setXMLInputStream(iStream);
     XTandemParameterSet xTandemParameterSet = xTandemParameterFileUtil.fetchXTandemParameterSet();
-    // Get XTandemParameterSetOptionsUtil instance
-    XTandemParameterSetOptionsUtil xTandemParameterSetOptionUtil = new XTandemParameterSetOptionsUtil();
-    // Get list path default parameters option data
-    List<String> listPathDefaultParametersStringList = xTandemParameterSetOptionUtil.fetchListPathDefaultParametersStringList();
-    List<Option> listPathDefaultParametersOptionList = stringListToOptionList(listPathDefaultParametersStringList);
-    // Get Eukaryotes species option data
-    List<String> speciesStringList = xTandemParameterSetOptionUtil.fetchSpeciesStringList();
-    List<Option> speciesOptionList = stringListToOptionList(speciesStringList);
-    // Get Prokaryotes species option data
-    List<String> proSpeciesStringList = xTandemParameterSetOptionUtil.fetchProSpeciesStringList();
-    List<Option> proSpeciesOptionList = stringListToOptionList(proSpeciesStringList);
-    // Get residue modification mass option data
-    List<String> residueModificationMassStringList = xTandemParameterSetOptionUtil.fetchResidueModificationMassStringList();
-    List<Option> residueModificationMassOptionList = stringListToOptionList(residueModificationMassStringList);
-    // Get residue potential modification mass option data
-    List<String> residuePotentialModificationMassStringList = xTandemParameterSetOptionUtil.fetchResiduePotentialModificationMassStringList();
-    List<Option> residuePotentialModificationMassOptionList = stringListToOptionList(residuePotentialModificationMassStringList);
-    // Get protein cleavage site option data
-    List<String> proteinCleavageSiteStringList = xTandemParameterSetOptionUtil.fetchProteinCleavageSiteStringList();
-    List<Option> proteinCleavageSiteOptionList = stringListToOptionList(proteinCleavageSiteStringList);
-    // Get refine potential modification mass option data
-    List<String> refinePotentialModificationMassStringList = xTandemParameterSetOptionUtil.fetchRefinePotentialModificationMassStringList();
-    List<Option> refinePotentialModificationMassOptionList = stringListToOptionList(refinePotentialModificationMassStringList);
-    // XTandem parameter set form
-    //Form xTandemParameterSetForm = getFormFactory().getXTandemParameterSetForm(xTandemParameterSet);
-    Form xTandemParameterSetForm = getXTandemParameterSetForm(xTandemParameterSet,
-      listPathDefaultParametersOptionList,
-      speciesOptionList,
-      proSpeciesOptionList,
-      residueModificationMassOptionList,
-      residuePotentialModificationMassOptionList,
-      proteinCleavageSiteOptionList,
-      refinePotentialModificationMassOptionList);
+    Form xTandemParameterSetForm = new XTandemParameterSetForm(xTandemParameterSet);
     /***********************************************************************
      * Annotations table
@@ -173 +139 @@
       for (Integer spectrumFileId : spectrumFileIds)
       {
-       getFormFactory().addHiddenField(xTandemParameterSetForm, SearchXTandem.VSPECTRUMFILEID, spectrumFileId);
+        getFormFactory().addHiddenField(xTandemParameterSetForm, SearchXTandem.VSPECTRUMFILEID, spectrumFileId);
       }
       searchXTandemViaWebInterface.addParameter(SearchXTandem.VXTANDEMUSEWEBINTERFACEFLAG, true);
@@ -220 +186 @@
     setLayout(layout);
   }
-
-
-  /**
-   * Converts a list of alternating key and value strings
-   * into a list of options.
-   * 
-   * @param stringList List<String> A list of alternating key and value strings.
-   * @return List<Option> A list of options
-   */
-  private List<Option> stringListToOptionList(List<String> stringList)
-  {
-    List<Option> optionList = new ArrayList<Option>(0);
-    for (int i = 0; i < stringList.size(); i = i + 2)
-    {
-      String key = stringList.get(i);
-      String value = stringList.get(i + 1);
-      /*
-       * Note that the option "value" corresponds
-       * to the "key" in the key-value string pair,
-       * while the option "content" corresponds
-       * to the "value" in the key-value string pair.
-       */
-      Option option = new Option(key, value);
-      optionList.add(option);
-    }
-    return optionList;
-  }
-
-  public Form getXTandemParameterSetForm(
-      XTandemParameterSet xTandemParameterSet,
-      List<Option> listPathDefaultParametersOptionList,
-      List<Option> speciesOptionList, List<Option> proSpeciesOptionList,
-      List<Option> residueModificationMassOptionList,
-      List<Option> residuePotentialModificationMassOptionList,
-      List<Option> proteinCleavageSiteOptionList,
-      List<Option> refinePotentialModificationMassOptionList)
-  {
-    // DbControl dc = project.getDbControl();
-    Form form = new Form("XTandemParameterSetForm");
-    /*
-     * String select box variables
-     */
-    VString validStringParam = null;
-    List<String> stringList = null;
-    List<Option> optionList = null;
-    String selected = null;
-    List<String> selectedList = null;
-    /*
-     * List path field set
-     */
-    Fieldset listPathFS = new Fieldset();
-    listPathFS.setTitle("XTandemParameterSetListPath");
-    form.addFieldset(listPathFS);
-    // List path, default parameters
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("/tandem/methods/fticr.xml", "FTICR (10 ppm)"));
-    optionList.add(new Option("/tandem/methods/qstar.xml",  "Quad-TOF (100 ppm)"));
-    optionList.add(new Option("/tandem/methods/qstar_l.xml",  "Quad-TOF (0.5 Da)"));
-    optionList.add(new Option("/tandem/methods/iontrap.xml",  "Ion Trap (4 Da)"));
-    // Use input list path default parameters option list if present
-    if (listPathDefaultParametersOptionList != null && listPathDefaultParametersOptionList.size() > 0)
-    {
-      optionList = listPathDefaultParametersOptionList;
-    }
-    selected = xTandemParameterSet.getListPathDefaultParameters();
-    Select<VString> listPathDefaultParametersSelectBox = new Select<VString>(validStringParam, optionList);
-  listPathDefaultParametersSelectBox.selectOption( selected);
-    listPathDefaultParametersSelectBox.setLabel("XTandemListPathDefaultParameters");
-    listPathDefaultParametersSelectBox.setMultiple(false);
-    int selectBoxSize = 4;
-    if (optionList.size() < selectBoxSize)
-    {
-      selectBoxSize = optionList.size();
-    }
-    listPathDefaultParametersSelectBox.setSize(selectBoxSize);
-    listPathFS.add(listPathDefaultParametersSelectBox);
-    // List path, taxonomy information
-    TextField<String> taxonomyInformationListPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION);
-    taxonomyInformationListPath.setValue(xTandemParameterSet
-      .getListPathTaxonomyInformation());
-    listPathFS.add(taxonomyInformationListPath);
-    /*
-     * Spectrum field set
-     */
-    Fieldset spectrumFS = new Fieldset();
-    spectrumFS.setTitle("XTandemParameterSetSpectrum");
-    form.addFieldset(spectrumFS);
-    // Spectrum, path
-    TextField<String> spectrumPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PATH);
-    spectrumPath.setValue(xTandemParameterSet.getSpectrumPath());
-    spectrumFS.add(spectrumPath);
-    // Spectrum, fragment monoisotopic mass error
-    TextField<String> fragMiMassError = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR);
-    fragMiMassError.setValue(xTandemParameterSet
-      .getSpectrumFragmentMonoisotopicMassError());
-    spectrumFS.add(fragMiMassError);
-    // Spectrum, parent monoisotopic mass error plus
-    TextField<String> parentMiMassErrorPlus = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS);
-    parentMiMassErrorPlus.setValue(xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassErrorPlus());
-    spectrumFS.add(parentMiMassErrorPlus);
-    // Spectrum, parent monoisotopic mass error minus
-    TextField<String> parentMiMassErrorMinus = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS);
-    parentMiMassErrorMinus.setValue(xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassErrorMinus());
-    spectrumFS.add(parentMiMassErrorMinus);
-    // Spectrum, parent monoisotopic mass isotope error
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassIsotopeError();
-    Select<VString> parentMiMassIsotopeError = new Select<VString>(validStringParam, stringList, selected);
-    spectrumFS.add(parentMiMassIsotopeError);
-    // Spectrum, fragment monoisotopic mass error units
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS;
-    stringList = new ArrayList<String>();
-    stringList.add("Daltons");
-    stringList.add("ppm");
-    selected = xTandemParameterSet
-      .getSpectrumFragmentMonoisotopicMassErrorUnits();
-    Select<VString> fragMiMassErrorUnits = new Select<VString>(validStringParam, stringList, selected);
-    spectrumFS.add(fragMiMassErrorUnits);
-    // Spectrum, parent monoisotopic mass error units
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS;
-    stringList = new ArrayList<String>();
-    stringList.add("Daltons");
-    stringList.add("ppm");
-    selected = xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassErrorUnits();
-    Select<VString> parentMiMassErrorUnits = new Select<VString>(validStringParam, stringList, selected);
-    spectrumFS.add(parentMiMassErrorUnits);
-    // Spectrum, fragment mass type
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_FRAG_MASS_TYPE;
-    stringList = new ArrayList<String>();
-    stringList.add("monoisotopic");
-    stringList.add("average");
-    selected = xTandemParameterSet.getSpectrumFragmentMassType();
-    Select<VString> fragMassType = new Select<VString>(validStringParam,  stringList, selected);
-    spectrumFS.add(fragMassType);
-    // Spectrum, dynamic range
-    TextField<String> dynamicRange = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_DYNAMIC_RANGE);
-    dynamicRange.setValue(xTandemParameterSet.getSpectrumDynamicRange());
-    spectrumFS.add(dynamicRange);
-    // Spectrum, total peaks
-    TextField<String> totalPeaks = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_TOTAL_PEAKS);
-    totalPeaks.setValue(xTandemParameterSet.getSpectrumTotalPeaks());
-    spectrumFS.add(totalPeaks);
-    // Spectrum, maximum parent charge
-    TextField<String> maxParentCharge = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE);
-    maxParentCharge.setValue(xTandemParameterSet
-      .getSpectrumMaximumParentCharge());
-    spectrumFS.add(maxParentCharge);
-    // Spectrum, use noise suppression
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getSpectrumUseNoiseSuppression();
-    Select<VString> useNoiseSuppression = new Select<VString>(validStringParam, stringList, selected);
-    spectrumFS.add(useNoiseSuppression);
-    // Spectrum, minimum parent m+h
-    TextField<String> minParentMPlusH = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H);
-    minParentMPlusH.setValue(xTandemParameterSet
-      .getSpectrumMinimumParentMPlusH());
-    spectrumFS.add(minParentMPlusH);
-    // Spectrum, maximum parent m+h
-    TextField<String> maxParentMPlusH = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H);
-    maxParentMPlusH.setValue(xTandemParameterSet
-      .getSpectrumMaximumParentMPlusH());
-    spectrumFS.add(maxParentMPlusH);
-    // Spectrum, minimum fragment mz
-    TextField<String> minFragmentMz = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MIN_FRAG_MZ);
-    minFragmentMz.setValue(xTandemParameterSet
-      .getSpectrumMinimumFragmentMz());
-    spectrumFS.add(minFragmentMz);
-    // Spectrum, minimum peaks
-    TextField<String> minPeaks = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MIN_PEAKS);
-    minPeaks.setValue(xTandemParameterSet.getSpectrumMinimumPeaks());
-    spectrumFS.add(minPeaks);
-    // Spectrum, threads
-    TextField<String> threads = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_THREADS);
-    threads.setValue(xTandemParameterSet.getSpectrumThreads());
-    spectrumFS.add(threads);
-    // Spectrum, sequence batch size
-    TextField<String> spectrumSequenceBatchSize = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE);
-    spectrumSequenceBatchSize.setValue(xTandemParameterSet
-      .getSpectrumSequenceBatchSize());
-    spectrumFS.add(spectrumSequenceBatchSize);
-    /*
-     * Residue field set
-     */
-    Fieldset residueFS = new Fieldset();
-    residueFS.setTitle("XTandemParameterSetResidue");
-    form.addFieldset(residueFS);
-    // Residue, modification mass select
-    /*
-     * Residue modification mass selection has one peculiarity: 1. The GUI
-     * selection is divided into one selection box and an entry field. A
-     * selection in the selection box will only be used if the entry field
-     * is empty.
-     */
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_MODIFICATION_MASS_SELECT;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("", "none"));
-    optionList.add(new Option("57.021464@C", "Carbamidomethyl (C)"));
-    optionList.add(new Option("442.224991@C", "ICAT-D (C)"));
-    optionList.add(new Option("227.126991@C", "ICAT-C (C)"));
-    optionList.add(new Option("58.005479@C", "Carboxymethyl (C)"));
-    optionList.add(new Option("105.057849@C", "Pyridylethyl (C)"));
-    optionList.add(new Option("71.037114@C", "Propionamide (C)"));
-    optionList.add(new Option("144.102063@[,144.102063@K",
-      "iTRAQ (N-term,K)"));
-    // Use input residue modification mass option list if present
-    if (residueModificationMassOptionList != null && residueModificationMassOptionList
-      .size() > 0)
-    {
-      optionList = residueModificationMassOptionList;
-    }
-    selected = xTandemParameterSet.getResidueModificationMass();
-    Select<VString> residueModificationMassSelectBox = new Select<VString>(
-      validStringParam, optionList);
-  residueModificationMassSelectBox.selectOption( selected);
-    residueModificationMassSelectBox
-      .setLabel("XTandemResidueModificationMassSelect");
-    residueFS.add(residueModificationMassSelectBox);
-    // Residue, modification mass (own entered value)
-    TextField<String> modificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_MODIFICATION_MASS);
-    modificationMass.setLabel("XTandemResidueModificationMassEnter");
-    // Only insert selected value if not found in select box
-    if (!itemInOptionList(optionList, selected))
-    {
-      log
-        .debug("residue modification mass, inserted value = \"" + xTandemParameterSet
-          .getResidueModificationMass() + "\"");
-      modificationMass.setValue(xTandemParameterSet
-        .getResidueModificationMass());
-    }
-    else
-    {
-
-      modificationMass.setValue("");
-    }
-    log
-      .debug("residue modification mass, modificationMass.getValue() = \"" + modificationMass
-        .getValue() + "\"");
-    residueFS.add(modificationMass);
-    // Residue, potential modification mass select
-    /*
-     * Residue potential modification mass selection has two peculiarities:
-     * 1. It supports selection of multiple items. 2. The GUI selection is
-     * divided into one multiple selection box and an entry field.
-     * Selections in the selection box will only be used if the entry field
-     * is empty. The multiple selection items are stored in XML as a string
-     * with items separated by ", ".
-     */
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("", "none"));
-    optionList.add(new Option("15.994915@M", "Oxidation (M)"));
-    optionList.add(new Option("15.994915@W", "Oxidation (W)"));
-    optionList.add(new Option("0.984016@N", "Deamidation (N)"));
-    optionList.add(new Option("0.984016@Q", "Deamidation (Q)"));
-    optionList.add(new Option("8.0502@C", "ICAT-D:2H(8) (C)"));
-    optionList.add(new Option("9.0302@C", "ICAT-C:13C(9) (C)"));
-    optionList.add(new Option("144.102063@[", "iTRAQ (N-term)"));
-    optionList.add(new Option("144.102063@K", "iTRAQ (K)"));
-    optionList.add(new Option("79.966331@S", "Phospho (S)"));
-    optionList.add(new Option("79.966331@T", "Phospho (T)"));
-    optionList.add(new Option("79.966331@Y", "Phospho (Y)"));
-    optionList.add(new Option("79.956815@Y", "Sulfo (Y)"));
-    optionList.add(new Option("42.010565@K", "Acetyl (K)"));
-    // Use input residue potential modification mass option list if present
-    if (residuePotentialModificationMassOptionList != null && residuePotentialModificationMassOptionList
-      .size() > 0)
-    {
-      optionList = residuePotentialModificationMassOptionList;
-      log
-        .debug("Input residue potential modification mass option list used");
-    }
-    else
-    {
-      log
-        .debug("Default residue potential modification mass option list used");
-    }
-    selected = xTandemParameterSet.getResiduePotentialModificationMass();
-    log
-      .debug("residue potential modification mass selected = \"" + selected + "\"");
-    selectedList = listStringToStringList(selected, ",");
-    log
-      .debug("residue potential modification mass selectedList = " + selectedList);
-    Select<VString> residuePotentialModificationMassSelectBox = new Select<VString>(
-      validStringParam, optionList, selectedList);
-    residuePotentialModificationMassSelectBox
-      .setLabel("XTandemResiduePotentialModificationMassSelect");
-    residuePotentialModificationMassSelectBox.setMultiple(true);
-    residuePotentialModificationMassSelectBox.setSize(4);
-    residueFS.add(residuePotentialModificationMassSelectBox);
-    // Residue, potential modification mass
-    TextField<String> potentialModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS);
-    potentialModificationMass
-      .setLabel("XTandemResiduePotentialModificationMassEnter");
-    potentialModificationMass.setValue(xTandemParameterSet
-      .getResiduePotentialModificationMass());
-    // Only insert selected values if not all found in select box
-    if (!allItemsInOptionList(optionList, selectedList))
-    {
-      log
-        .debug("residue potential modification mass, inserted value = \"" + xTandemParameterSet
-          .getResiduePotentialModificationMass() + "\"");
-      potentialModificationMass.setValue(xTandemParameterSet
-        .getResiduePotentialModificationMass());
-    }
-    else
-    {
-      potentialModificationMass.setValue("");
-    }
-    residueFS.add(potentialModificationMass);
-    // Residue, potential modification motif
-    TextField<String> potentialModificationMotif = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF);
-    potentialModificationMotif.setValue(xTandemParameterSet
-      .getResiduePotentialModificationMotif());
-    residueFS.add(potentialModificationMotif);
-    /*
-     * Protein field set
-     */
-    Fieldset proteinFS = new Fieldset();
-    proteinFS.setTitle("XTandemParameterSetProtein");
-    form.addFieldset(proteinFS);
-    // Protein, taxon
-    /*
-     * Taxonomy selection has two peculiarities: 1. It supports selection of
-     * multiple items. 2. The GUI selection is divided into two multiple
-     * selection boxes. The multiple selection items are stored in XML as a
-     * string with items separated by ", ".
-     */
-    // Taxon - Eukaryotes
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_TAXON;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("", "none"));
-    optionList.add(new Option("human", "H. sapiens (human)"));
-    optionList.add(new Option("mouse", "M. musculus (mouse)"));
-    optionList.add(new Option("rat", "R. norvegicus (rat)"));
-    optionList.add(new Option("yeast", "S. cerevisiae (budding yeast)"));
-    optionList.add(new Option("", "------------------"));
-    optionList.add(new Option("mosquito", "A. gambiae (mosquito)"));
-    optionList.add(new Option("aspergillus_fumigatus",
-      "A. fumigatus (mould)"));
-    optionList.add(new Option("bee", "A. mellifera (honey bee)"));
-    optionList.add(new Option("thalecress", "A. thaliana (thale cress)"));
-    optionList.add(new Option("cow", "B. taurus (cow)"));
-    optionList.add(new Option("dog", "C. familiaris (dog)"));
-    optionList.add(new Option("worm", "C. elegans (round worm)"));
-    optionList.add(new Option("zebrafish", "D. rerio (zebra fish)"));
-    optionList.add(new Option("fly", "D. melanogaster (fruit fly)"));
-    optionList.add(new Option("chicken", "G. gallus (hen)"));
-    optionList.add(new Option("human", "H. sapiens (human)"));
-    optionList.add(new Option("mouse", "M. musculus (mouse)"));
-    optionList.add(new Option("rice", "O.sativa (rice)"));
-    optionList.add(new Option("rat", "R. norvegicus (rat)"));
-    optionList.add(new Option("spombe", "S. pombe (fission yeast)"));
-    optionList.add(new Option("yeast", "S. cerevisiae (budding yeast)"));
-    optionList.add(new Option("frog", "S. tropicalis (toad)"));
-    // Use input species option list if present
-    if (speciesOptionList != null && speciesOptionList.size() > 0)
-    {
-      optionList = speciesOptionList;
-    }
-    selected = xTandemParameterSet.getProteinTaxon();
-    selectedList = listStringToStringList(selected, ",\\ ");
-    Select<VString> taxon = new Select<VString>(validStringParam,
-      optionList, selectedList);
-    taxon.setLabel("XTandemProteinTaxonEukaryotes");
-    taxon.setMultiple(true);
-    taxon.setSize(5);
-    proteinFS.add(taxon);
-    // Taxon - Prokaryotes
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_TAXON1;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("", "none"));
-    optionList.add(new Option("Bacillus_subtilis", "Bacillus subtilis"));
-    optionList.add(new Option("Clostridium_perfringens",
-      "Clostridium perfringens"));
-    optionList.add(new Option("Deinococcus_radiodurans",
-      "Deinococcus radiodurans"));
-    optionList.add(new Option("Escherichia_coli_K12",
-      "Escherichia coli K12"));
-    optionList.add(new Option("Francisella_tularensis_tularensis",
-      "Francisella tularensis tularensis"));
-    optionList.add(new Option("Geobacter_sulfurreducens",
-      "Geobacter sulfurreducens"));
-    optionList.add(new Option("Haemophilus_influenzae",
-      "Haemophilus influenzae"));
-    optionList.add(new Option("Listeria_innocua", "Listeria innocua"));
-    optionList.add(new Option("Mycobacterium_leprae",
-      "Mycobacterium leprae"));
-    optionList.add(new Option("Mycobacterium_tuberculosis_CDC1551",
-      "Mycobacterium tuberculosis CDC1551"));
-    optionList
-      .add(new Option("Mycoplasma_pulmonis", "Mycoplasma pulmonis"));
-    optionList.add(new Option("Staphylococcus_aureus_MW2",
-      "Staphylococcus aureus MW2"));
-    optionList.add(new Option("Streptococcus_pneumoniae_TIGR4",
-      "Streptococcus pneumoniae TIGR4"));
-    optionList.add(new Option("Streptococcus_pyogenes_M1_GAS",
-      "Streptococcus pyogenes M1 GAS"));
-    optionList.add(new Option("Yersinia_pestis_CO92",
-      "Yersinia pestis CO92"));
-    // Use input species option list if present
-    if (proSpeciesOptionList != null && proSpeciesOptionList.size() > 0)
-    {
-      optionList = proSpeciesOptionList;
-    }
-    // Same selection list as for Eukaryotes taxon is used for Prokaryotes
-    Select<VString> taxon1 = new Select<VString>(validStringParam,
-      optionList, selectedList);
-    taxon1.setLabel("XTandemProteinTaxonProkaryotes");
-    taxon1.setMultiple(true);
-    taxon1.setSize(5);
-    proteinFS.add(taxon1);
-    // Protein, cleavage site
-    /*
-     * Protein cleavage site selection has one peculiarity: 1. The GUI
-     * selection is divided into one selection box and an entry field. A
-     * selection in the selection box will only be used if the entry field
-     * is empty.
-     */
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_CLEAVAGE_SITE_SELECT;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("[RK]|{P}", "trypsin, [RK]|{P}"));
-    optionList.add(new Option("[R]|[X]", "endo-arg-C, [R]|[X]"));
-    optionList.add(new Option("[K]|[X]", "endo-lys-C, [K]|[X]"));
-    optionList.add(new Option("[E]|[X]", "endo-glu-C, [E]|[X]"));
-    optionList.add(new Option("[X]|[D]", "endo-asp-N, [X]|[D]"));
-    optionList.add(new Option("[ED]|[X]", "V8, [ED]|[X]"));
-    // Use input protein cleavage site option list if present
-    if (proteinCleavageSiteOptionList != null && proteinCleavageSiteOptionList
-      .size() > 0)
-    {
-      optionList = proteinCleavageSiteOptionList;
-    }
-    selected = xTandemParameterSet.getProteinCleavageSite();
-    Select<VString> proteinCleavageSiteSelectBox = new Select<VString>(
-      validStringParam, optionList);
-  proteinCleavageSiteSelectBox.selectOption( selected);
-    proteinCleavageSiteSelectBox
-      .setLabel("XTandemProteinCleavageSiteSelect");
-    proteinFS.add(proteinCleavageSiteSelectBox);
-    // Protein, cleavage site (own entered value)
-    TextField<String> cleavageSite = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_CLEAVAGE_SITE);
-    cleavageSite.setLabel("XTandemProteinCleavageSiteEnter");
-    // Only insert selected value if not found in select box
-    if (!itemInOptionList(optionList, selected))
-    {
-      cleavageSite.setValue(xTandemParameterSet.getProteinCleavageSite());
-    }
-    else
-    {
-      cleavageSite.setValue("");
-    }
-    proteinFS.add(cleavageSite);
-    // Protein, modified residue mass file
-    TextField<String> proteinModifiedResidueMassFile = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE);
-    proteinModifiedResidueMassFile.setValue(xTandemParameterSet
-      .getProteinModifiedResidueMassFile());
-    proteinFS.add(proteinModifiedResidueMassFile);
-    // Protein, cleavage N-terminal mass change
-    TextField<String> proteinCleavageNTerminalMassChange = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE);
-    proteinCleavageNTerminalMassChange.setValue(xTandemParameterSet
-      .getProteinCleavageNTerminalMassChange());
-    proteinFS.add(proteinCleavageNTerminalMassChange);
-    // Protein, cleavage C-terminal mass change
-    TextField<String> proteinCleavageCTerminalMassChange = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE);
-    proteinCleavageCTerminalMassChange.setValue(xTandemParameterSet
-      .getProteinCleavageCTerminalMassChange());
-    proteinFS.add(proteinCleavageCTerminalMassChange);
-    // Protein, N-terminal residue modification mass
-    TextField<String> nTerminalResidueModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS);
-    nTerminalResidueModificationMass.setValue(xTandemParameterSet
-      .getProteinNTerminalResidueModificationMass());
-    proteinFS.add(nTerminalResidueModificationMass);
-    // Protein, C-terminal residue modification mass
-    TextField<String> cTerminalResidueModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS);
-    cTerminalResidueModificationMass.setValue(xTandemParameterSet
-      .getProteinCTerminalResidueModificationMass());
-    proteinFS.add(cTerminalResidueModificationMass);
-    // Protein, homolog management
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getProteinHomologManagement();
-    Select<VString> homologManagement = new Select<VString>(validStringParam, stringList, selected);
-    proteinFS.add(homologManagement);
-    /*
-     * Refine field set
-     */
-    Fieldset refineFS = new Fieldset();
-    refineFS.setTitle("XTandemParameterSetRefine");
-    form.addFieldset(refineFS);
-    // Refine
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_REFINE;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getRefine();
-    Select<VString> refine = new Select<VString>(validStringParam,  stringList, selected);
-    refineFS.add(refine);
-    // Refine, modification mass
-    TextField<String> refineModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_MODIFICATION_MASS);
-    refineModificationMass.setValue(xTandemParameterSet
-      .getRefineModificationMass());
-    refineFS.add(refineModificationMass);
-    // Refine, sequence path
-    TextField<String> refineSequencePath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_SEQUENCE_PATH);
-    refineSequencePath
-      .setValue(xTandemParameterSet.getRefineSequencePath());
-    refineFS.add(refineSequencePath);
-    // Refine, tic percent
-    TextField<String> refineTicPercent = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_TIC_PERCENT);
-    refineTicPercent.setValue(xTandemParameterSet.getRefineTicPercent());
-    refineFS.add(refineTicPercent);
-    // Refine, spectrum synthesis
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_REFINE_SPECTRUM_SYNTHESIS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getRefineSpectrumSynthesis();
-    Select<VString> spectrumSynthesis = new Select<VString>(validStringParam, stringList, selected);
-    refineFS.add(spectrumSynthesis);
-    // Refine, maximum valid expectation value
-    TextField<String> maxValidExpectationValue = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE);
-    maxValidExpectationValue.setValue(xTandemParameterSet
-      .getRefineMaximumValidExpectationValue());
-    refineFS.add(maxValidExpectationValue);
-    // Refine, potential N-terminus modifications
-    TextField<String> potentialNTerminusModifications = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS);
-    potentialNTerminusModifications.setValue(xTandemParameterSet
-      .getRefinePotentialNTerminusModifications());
-    refineFS.add(potentialNTerminusModifications);
-    // Refine, potential C-terminus modifications
-    TextField<String> potentialCTerminusModifications = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS);
-    potentialCTerminusModifications.setValue(xTandemParameterSet
-      .getRefinePotentialCTerminusModifications());
-    refineFS.add(potentialCTerminusModifications);
-    // Refine, unanticipated cleavage
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getRefineUnanticipatedCleavage();
-    Select<VString> unanticipatedCleavage = new Select<VString>(validStringParam, stringList, selected);
-    refineFS.add(unanticipatedCleavage);
-    // Refine, potential modification mass select
-    /*
-     * Refine potential modification mass selection has two peculiarities:
-     * 1. It supports selection of multiple items. 2. The GUI selection is
-     * divided into one multiple selection box and an entry field.
-     * Selections in the selection box will only be used if the entry field
-     * is empty. The multiple selection items are stored in XML as a string
-     * with items separated by ", ".
-     */
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("", "none"));
-    optionList.add(new Option("15.994915@M", "Oxidation (M)"));
-    optionList.add(new Option("15.994915@W", "Oxidation (W)"));
-    optionList.add(new Option("0.984016@N", "Deamidation (N)"));
-    optionList.add(new Option("0.984016@Q", "Deamidation (Q)"));
-    optionList.add(new Option("8.0502@C", "ICAT-D:2H(8) (C)"));
-    optionList.add(new Option("9.0302@C", "ICAT-C:13C(9) (C)"));
-    optionList.add(new Option("144.102063@[", "iTRAQ (N-term)"));
-    optionList.add(new Option("144.102063@K", "iTRAQ (K)"));
-    optionList.add(new Option("79.966331@S", "Phospho (S)"));
-    optionList.add(new Option("79.966331@T", "Phospho (T)"));
-    optionList.add(new Option("79.966331@Y", "Phospho (Y)"));
-    optionList.add(new Option("79.956815@Y", "Sulfo (Y)"));
-    optionList.add(new Option("42.010565@K", "Acetyl (K)"));
-    // Use input refine potential modification mass option list if present
-    if (refinePotentialModificationMassOptionList != null && refinePotentialModificationMassOptionList
-      .size() > 0)
-    {
-      optionList = refinePotentialModificationMassOptionList;
-      log
-        .debug("Input refine potential modification mass option list used");
-    }
-    else
-    {
-      log
-        .debug("Default refine potential modification mass option list used");
-    }
-    selected = xTandemParameterSet.getRefinePotentialModificationMass();
-    log
-      .debug("refine potential modification mass selected = \"" + selected + "\"");
-    selectedList = listStringToStringList(selected, ",");
-    log
-      .debug("refine potential modification mass selectedList = " + selectedList);
-    Select<VString> refinePotentialModificationMassSelectBox = new Select<VString>(
-      validStringParam, optionList, selectedList);
-    refinePotentialModificationMassSelectBox
-      .setLabel("XTandemRefinePotentialModificationMassSelect");
-    refinePotentialModificationMassSelectBox.setMultiple(true);
-    refinePotentialModificationMassSelectBox.setSize(4);
-    refineFS.add(refinePotentialModificationMassSelectBox);
-    // Refine, potential modification mass
-    TextField<String> refinePotentialModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS);
-    refinePotentialModificationMass
-      .setLabel("XTandemRefinePotentialModificationMassEnter");
-    refinePotentialModificationMass.setValue(xTandemParameterSet
-      .getRefinePotentialModificationMass());
-    // Only insert selected values if not all found in select box
-    if (!allItemsInOptionList(optionList, selectedList))
-    {
-      log
-        .debug("refine potential modification mass, inserted value = \"" + xTandemParameterSet
-          .getRefinePotentialModificationMass() + "\"");
-      refinePotentialModificationMass.setValue(xTandemParameterSet
-        .getRefinePotentialModificationMass());
-    }
-    else
-    {
-      refinePotentialModificationMass.setValue("");
-    }
-    refineFS.add(refinePotentialModificationMass);
-    /** **************************************** */
-    // Refine, point mutations
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POINT_MUTATIONS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getRefinePointMutations();
-    Select<VString> pointMutations = new Select<VString>(validStringParam,  stringList, selected);
-    refineFS.add(pointMutations);
-    // Refine, use potential modifications for full refinement
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet
-      .getRefineUsePotentialModificationsForFullRefinement();
-    Select<VString> usePotentialModificationsForFullRefinement = new Select<VString>(validStringParam, stringList, selected);
-    refineFS.add(usePotentialModificationsForFullRefinement);
-    // Refine, potential modification motif
-    TextField<String> potentialModificationMotifRefine = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF);
-    potentialModificationMotifRefine.setValue(xTandemParameterSet
-      .getRefinePotentialModificationMotif());
-    refineFS.add(potentialModificationMotifRefine);
-    /*
-     * Scoring field set
-     */
-    Fieldset scoringFS = new Fieldset();
-    scoringFS.setTitle("XTandemParameterSetScoring");
-    form.addFieldset(scoringFS);
-    // Scoring, minimum ion count
-    TextField<String> minIonCount = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_MIN_ION_COUNT);
-    minIonCount.setValue(xTandemParameterSet.getScoringMinimumIonCount());
-    scoringFS.add(minIonCount);
-    // Scoring, maximum missed cleavage sites
-    TextField<String> maxMissedCleavageSites = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES);
-    maxMissedCleavageSites.setValue(xTandemParameterSet
-      .getScoringMaximumMissedCleavageSites());
-    scoringFS.add(maxMissedCleavageSites);
-    // Scoring, x ions
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_X_IONS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringXIons();
-    Select<VString> xIons = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(xIons);
-    // Scoring, y ions
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_Y_IONS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringYIons();
-    Select<VString> yIons = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(yIons);
-    // Scoring, z ions
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_Z_IONS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringZIons();
-    Select<VString> zIons = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(zIons);
-    // Scoring, a ions
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_A_IONS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringAIons();
-    Select<VString> aIons = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(aIons);
-    // Scoring, b ions
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_B_IONS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringBIons();
-    Select<VString> bIons = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(bIons);
-    // Scoring, c ions
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_C_IONS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringCIons();
-    Select<VString> cIons = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(cIons);
-    // Scoring, cyclic permutation
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_CYCLIC_PERMUTATION;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringCyclicPermutation();
-    Select<VString> cyclicPermutation = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(cyclicPermutation);
-    // Scoring, include reverse
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_INCLUDE_REVERSE;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getScoringIncludeReverse();
-    Select<VString> includeReverse = new Select<VString>(validStringParam, stringList, selected);
-    scoringFS.add(includeReverse);
-    // Scoring, algorithm
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_SCORING_ALGORITHM;
-    optionList = new ArrayList<Option>();
-    optionList.add(new Option("", "native"));
-    optionList.add(new Option("k-score", "k-score"));
-    selected = xTandemParameterSet.getScoringAlgorithm();
-    Select<VString> algorithmSelectBox = new Select<VString>(
-      validStringParam, optionList);
-  algorithmSelectBox.selectOption( selected);
-    scoringFS.add(algorithmSelectBox);
-    /*
-     * Output field set
-     */
-    Fieldset outputFS = new Fieldset();
-    outputFS.setTitle("XTandemParameterSetOutput");
-    form.addFieldset(outputFS);
-    // Output, path
-    TextField<String> outputPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PATH);
-    outputPath.setValue(xTandemParameterSet.getOutputPath());
-    outputFS.add(outputPath);
-    // Output, log path
-    TextField<String> outputLogPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_LOG_PATH);
-    outputLogPath.setValue(xTandemParameterSet.getOutputLogPath());
-    outputFS.add(outputLogPath);
-    // Output, message
-    TextField<String> outputMessage = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_MESSAGE);
-    outputMessage.setValue(xTandemParameterSet.getOutputMessage());
-    outputFS.add(outputMessage);
-    // Output, sequence path
-    TextField<String> outputSequencePath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SEQUENCE_PATH);
-    outputSequencePath
-      .setValue(xTandemParameterSet.getOutputSequencePath());
-    outputFS.add(outputSequencePath);
-    // Output, sort results by
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SORT_RESULTS_BY;
-    stringList = new ArrayList<String>();
-    stringList.add("protein");
-    stringList.add("spectrum");
-    selected = xTandemParameterSet.getOutputSortResultsBy();
-    Select<VString> outputSortResultsBy = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(outputSortResultsBy);
-    // Output, path hashing
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PATH_HASHING;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputPathHashing();
-    Select<VString> pathHashing = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(pathHashing);
-    // Output, xsl path
-    TextField<String> xslPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_XSL_PATH);
-    xslPath.setValue(xTandemParameterSet.getOutputXslPath());
-    outputFS.add(xslPath);
-    // Output, parameters
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PARAMETERS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputParameters();
-    Select<VString> parameters = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(parameters);
-    // Output, performance
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PERFORMANCE;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputPerformance();
-    Select<VString> performance = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(performance);
-    // Output, spectra
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SPECTRA;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputSpectra();
-    Select<VString> spectra = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(spectra);
-    // Output, histograms
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_HISTOGRAMS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputHistograms();
-    Select<VString> histograms = new Select<VString>(validStringParam,  stringList, selected);
-    outputFS.add(histograms);
-    // Output, proteins
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PROTEINS;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputProteins();
-    Select<VString> proteins = new Select<VString>(validStringParam,  stringList, selected);
-    outputFS.add(proteins);
-    // Output, sequences
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SEQUENCES;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputSequences();
-    Select<VString> sequences = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(sequences);
-    // Output, one sequence copy
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY;
-    stringList = new ArrayList<String>();
-    stringList.add("yes");
-    stringList.add("no");
-    selected = xTandemParameterSet.getOutputOneSequenceCopy();
-    Select<VString> oneSequenceCopy = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(oneSequenceCopy);
-    // Output, results
-    validStringParam = SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_RESULTS;
-    stringList = new ArrayList<String>();
-    stringList.add("all");
-    stringList.add("valid");
-    stringList.add("stochastic");
-    selected = xTandemParameterSet.getOutputResults();
-    Select<VString> results = new Select<VString>(validStringParam, stringList, selected);
-    outputFS.add(results);
-    // Output, maximum valid expectation value
-    TextField<String> outputMaxValidExpectationValue = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE);
-    outputMaxValidExpectationValue.setValue(xTandemParameterSet
-      .getOutputMaximumValidExpectationValue());
-    outputFS.add(outputMaxValidExpectationValue);
-    // Output, histogram column width
-    TextField<String> histogramColumnWidth = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH);
-    histogramColumnWidth.setValue(xTandemParameterSet
-      .getOutputHistogramColumnWidth());
-    outputFS.add(histogramColumnWidth);
-    //
-    return form;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet fields to a Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // List path fields
-    fs = addXTandemParameterSetListPathFieldsToFieldset(
-      xTandemParameterSet, fs, fieldsHidden, fieldsDisabled);
-    // Spectrum fields
-    fs = addXTandemParameterSetSpectrumFieldsToFieldset(
-      xTandemParameterSet, fs, fieldsHidden, fieldsDisabled);
-    // Residue fields
-    fs = addXTandemParameterSetResidueFieldsToFieldset(xTandemParameterSet,
-      fs, fieldsHidden, fieldsDisabled);
-    // Protein fields
-    fs = addXTandemParameterSetProteinFieldsToFieldset(xTandemParameterSet,
-      fs, fieldsHidden, fieldsDisabled);
-    // Refine fields
-    fs = addXTandemParameterSetRefineFieldsToFieldset(xTandemParameterSet,
-      fs, fieldsHidden, fieldsDisabled);
-    // Scoring fields
-    fs = addXTandemParameterSetScoringFieldsToFieldset(xTandemParameterSet,
-      fs, fieldsHidden, fieldsDisabled);
-    // Output fields
-    fs = addXTandemParameterSetOutputFieldsToFieldset(xTandemParameterSet,
-      fs, fieldsHidden, fieldsDisabled);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet list path fields to a
-   * Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetListPathFieldsToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // List path, default parameters
-    TextField<String> defaultParametersListPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS);
-    defaultParametersListPath.setHidden(fieldsHidden);
-    defaultParametersListPath.setDisabled(fieldsDisabled);
-    defaultParametersListPath.setValue(xTandemParameterSet
-      .getListPathDefaultParameters());
-    fs.add(defaultParametersListPath);
-    // List path, taxonomy information
-    TextField<String> taxonomyInformationListPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION);
-    taxonomyInformationListPath.setHidden(fieldsHidden);
-    taxonomyInformationListPath.setDisabled(fieldsDisabled);
-    taxonomyInformationListPath.setValue(xTandemParameterSet
-      .getListPathTaxonomyInformation());
-    fs.add(taxonomyInformationListPath);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet spectrum fields to a
-   * Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetSpectrumFieldsToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // Spectrum, path
-    TextField<String> spectrumPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PATH);
-    spectrumPath.setHidden(fieldsHidden);
-    spectrumPath.setDisabled(fieldsDisabled);
-    spectrumPath.setValue(xTandemParameterSet.getSpectrumPath());
-    fs.add(spectrumPath);
-    // Spectrum, fragment monoisotopic mass error
-    TextField<String> fragMiMassError = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR);
-    fragMiMassError.setHidden(fieldsHidden);
-    fragMiMassError.setDisabled(fieldsDisabled);
-    fragMiMassError.setValue(xTandemParameterSet
-      .getSpectrumFragmentMonoisotopicMassError());
-    fs.add(fragMiMassError);
-    // Spectrum, parent monoisotopic mass error plus
-    TextField<String> parentMiMassErrorPlus = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS);
-    parentMiMassErrorPlus.setHidden(fieldsHidden);
-    parentMiMassErrorPlus.setDisabled(fieldsDisabled);
-    parentMiMassErrorPlus.setValue(xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassErrorPlus());
-    fs.add(parentMiMassErrorPlus);
-    // Spectrum, parent monoisotopic mass error minus
-    TextField<String> parentMiMassErrorMinus = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS);
-    parentMiMassErrorMinus.setHidden(fieldsHidden);
-    parentMiMassErrorMinus.setDisabled(fieldsDisabled);
-    parentMiMassErrorMinus.setValue(xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassErrorMinus());
-    fs.add(parentMiMassErrorMinus);
-    // Spectrum, parent monoisotopic mass isotope error
-    TextField<String> parentMiMassIsotopeError = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR);
-    parentMiMassIsotopeError.setHidden(fieldsHidden);
-    parentMiMassIsotopeError.setDisabled(fieldsDisabled);
-    parentMiMassIsotopeError.setValue(xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassIsotopeError());
-    fs.add(parentMiMassIsotopeError);
-    // Spectrum, fragment monoisotopic mass error units
-    TextField<String> fragMiMassErrorUnits = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS);
-    fragMiMassErrorUnits.setHidden(fieldsHidden);
-    fragMiMassErrorUnits.setDisabled(fieldsDisabled);
-    fragMiMassErrorUnits.setValue(xTandemParameterSet
-      .getSpectrumFragmentMonoisotopicMassErrorUnits());
-    fs.add(fragMiMassErrorUnits);
-    // Spectrum, parent monoisotopic mass error units
-    TextField<String> parentMiMassErrorUnits = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS);
-    parentMiMassErrorUnits.setHidden(fieldsHidden);
-    parentMiMassErrorUnits.setDisabled(fieldsDisabled);
-    parentMiMassErrorUnits.setValue(xTandemParameterSet
-      .getSpectrumParentMonoisotopicMassErrorUnits());
-    fs.add(parentMiMassErrorUnits);
-    // Spectrum, fragment mass type
-    TextField<String> fragMassType = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_FRAG_MASS_TYPE);
-    fragMassType.setHidden(fieldsHidden);
-    fragMassType.setDisabled(fieldsDisabled);
-    fragMassType
-      .setValue(xTandemParameterSet.getSpectrumFragmentMassType());
-    fs.add(fragMassType);
-    // Spectrum, dynamic range
-    TextField<String> dynamicRange = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_DYNAMIC_RANGE);
-    dynamicRange.setHidden(fieldsHidden);
-    dynamicRange.setDisabled(fieldsDisabled);
-    dynamicRange.setValue(xTandemParameterSet.getSpectrumDynamicRange());
-    fs.add(dynamicRange);
-    // Spectrum, total peaks
-    TextField<String> totalPeaks = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_TOTAL_PEAKS);
-    totalPeaks.setHidden(fieldsHidden);
-    totalPeaks.setDisabled(fieldsDisabled);
-    totalPeaks.setValue(xTandemParameterSet.getSpectrumTotalPeaks());
-    fs.add(totalPeaks);
-    // Spectrum, maximum parent charge
-    TextField<String> maxParentCharge = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE);
-    maxParentCharge.setHidden(fieldsHidden);
-    maxParentCharge.setDisabled(fieldsDisabled);
-    maxParentCharge.setValue(xTandemParameterSet
-      .getSpectrumMaximumParentCharge());
-    fs.add(maxParentCharge);
-    // Spectrum, use noise suppression
-    TextField<String> useNoiseSuppression = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION);
-    useNoiseSuppression.setHidden(fieldsHidden);
-    useNoiseSuppression.setDisabled(fieldsDisabled);
-    useNoiseSuppression.setValue(xTandemParameterSet
-      .getSpectrumUseNoiseSuppression());
-    fs.add(useNoiseSuppression);
-    // Spectrum, minimum parent m+h
-    TextField<String> minParentMPlusH = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H);
-    minParentMPlusH.setHidden(fieldsHidden);
-    minParentMPlusH.setDisabled(fieldsDisabled);
-    minParentMPlusH.setValue(xTandemParameterSet
-      .getSpectrumMinimumParentMPlusH());
-    fs.add(minParentMPlusH);
-    // Spectrum, maximum parent m+h
-    TextField<String> maxParentMPlusH = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H);
-    maxParentMPlusH.setHidden(fieldsHidden);
-    maxParentMPlusH.setDisabled(fieldsDisabled);
-    maxParentMPlusH.setValue(xTandemParameterSet
-      .getSpectrumMaximumParentMPlusH());
-    fs.add(maxParentMPlusH);
-    // Spectrum, minimum fragment mz
-    TextField<String> minFragmentMz = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MIN_FRAG_MZ);
-    minFragmentMz.setHidden(fieldsHidden);
-    minFragmentMz.setDisabled(fieldsDisabled);
-    minFragmentMz.setValue(xTandemParameterSet
-      .getSpectrumMinimumFragmentMz());
-    fs.add(minFragmentMz);
-    // Spectrum, minimum peaks
-    TextField<String> minPeaks = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_MIN_PEAKS);
-    minPeaks.setHidden(fieldsHidden);
-    minPeaks.setDisabled(fieldsDisabled);
-    minPeaks.setValue(xTandemParameterSet.getSpectrumMinimumPeaks());
-    fs.add(minPeaks);
-    // Spectrum, threads
-    TextField<String> threads = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_THREADS);
-    threads.setHidden(fieldsHidden);
-    threads.setDisabled(fieldsDisabled);
-    threads.setValue(xTandemParameterSet.getSpectrumThreads());
-    fs.add(threads);
-    // Spectrum, sequence batch size
-    TextField<String> spectrumSequenceBatchSize = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE);
-    spectrumSequenceBatchSize.setHidden(fieldsHidden);
-    spectrumSequenceBatchSize.setDisabled(fieldsDisabled);
-    spectrumSequenceBatchSize.setValue(xTandemParameterSet
-      .getSpectrumSequenceBatchSize());
-    fs.add(spectrumSequenceBatchSize);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet residue fields to a
-   * Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetResidueFieldsToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // Residue, modification mass
-    TextField<String> modificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_MODIFICATION_MASS);
-    modificationMass.setHidden(fieldsHidden);
-    modificationMass.setDisabled(fieldsDisabled);
-    modificationMass.setValue(xTandemParameterSet
-      .getResidueModificationMass());
-    fs.add(modificationMass);
-    // Residue, potential modification mass
-    TextField<String> potentialModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS);
-    potentialModificationMass.setHidden(fieldsHidden);
-    potentialModificationMass.setDisabled(fieldsDisabled);
-    potentialModificationMass.setValue(xTandemParameterSet
-      .getResiduePotentialModificationMass());
-    fs.add(potentialModificationMass);
-    // Residue, potential modification motif
-    TextField<String> potentialModificationMotif = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF);
-    potentialModificationMotif.setHidden(fieldsHidden);
-    potentialModificationMotif.setDisabled(fieldsDisabled);
-    potentialModificationMotif.setValue(xTandemParameterSet
-      .getResiduePotentialModificationMotif());
-    fs.add(potentialModificationMotif);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet protein fields to a
-   * Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetProteinFieldsToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // Protein, taxon
-    TextField<String> taxon = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_TAXON);
-    taxon.setHidden(fieldsHidden);
-    taxon.setDisabled(fieldsDisabled);
-    taxon.setValue(xTandemParameterSet.getProteinTaxon());
-    fs.add(taxon);
-    // Protein, cleavage site
-    TextField<String> cleavageSite = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_CLEAVAGE_SITE);
-    cleavageSite.setHidden(fieldsHidden);
-    cleavageSite.setDisabled(fieldsDisabled);
-    cleavageSite.setValue(xTandemParameterSet.getProteinCleavageSite());
-    fs.add(cleavageSite);
-    // Protein, modified residue mass file
-    TextField<String> proteinModifiedResidueMassFile = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE);
-    proteinModifiedResidueMassFile.setHidden(fieldsHidden);
-    proteinModifiedResidueMassFile.setDisabled(fieldsDisabled);
-    proteinModifiedResidueMassFile.setValue(xTandemParameterSet
-      .getProteinModifiedResidueMassFile());
-    fs.add(proteinModifiedResidueMassFile);
-    // Protein, cleavage N-terminal mass change
-    TextField<String> proteinCleavageNTerminalMassChange = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE);
-    proteinCleavageNTerminalMassChange.setHidden(fieldsHidden);
-    proteinCleavageNTerminalMassChange.setDisabled(fieldsDisabled);
-    proteinCleavageNTerminalMassChange.setValue(xTandemParameterSet
-      .getProteinCleavageNTerminalMassChange());
-    fs.add(proteinCleavageNTerminalMassChange);
-    // Protein, cleavage C-terminal mass change
-    TextField<String> proteinCleavageCTerminalMassChange = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE);
-    proteinCleavageCTerminalMassChange.setHidden(fieldsHidden);
-    proteinCleavageCTerminalMassChange.setDisabled(fieldsDisabled);
-    proteinCleavageCTerminalMassChange.setValue(xTandemParameterSet
-      .getProteinCleavageCTerminalMassChange());
-    fs.add(proteinCleavageCTerminalMassChange);
-    // Protein, N-terminal residue modification mass
-    TextField<String> nTerminalResidueModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS);
-    nTerminalResidueModificationMass.setHidden(fieldsHidden);
-    nTerminalResidueModificationMass.setDisabled(fieldsDisabled);
-    nTerminalResidueModificationMass.setValue(xTandemParameterSet
-      .getProteinNTerminalResidueModificationMass());
-    fs.add(nTerminalResidueModificationMass);
-    // Protein, C-terminal residue modification mass
-    TextField<String> cTerminalResidueModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS);
-    cTerminalResidueModificationMass.setHidden(fieldsHidden);
-    cTerminalResidueModificationMass.setDisabled(fieldsDisabled);
-    cTerminalResidueModificationMass.setValue(xTandemParameterSet
-      .getProteinCTerminalResidueModificationMass());
-    fs.add(cTerminalResidueModificationMass);
-    // Protein, homolog management
-    TextField<String> homologManagement = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT);
-    homologManagement.setHidden(fieldsHidden);
-    homologManagement.setDisabled(fieldsDisabled);
-    homologManagement.setValue(xTandemParameterSet
-      .getProteinHomologManagement());
-    fs.add(homologManagement);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet refine fields to a
-   * Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetRefineFieldsToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // Refine
-    TextField<String> refine = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE);
-    refine.setHidden(fieldsHidden);
-    refine.setDisabled(fieldsDisabled);
-    refine.setValue(xTandemParameterSet.getRefine());
-    fs.add(refine);
-    // Refine, modification mass
-    TextField<String> refineModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_MODIFICATION_MASS);
-    refineModificationMass.setHidden(fieldsHidden);
-    refineModificationMass.setDisabled(fieldsDisabled);
-    refineModificationMass.setValue(xTandemParameterSet
-      .getRefineModificationMass());
-    fs.add(refineModificationMass);
-    // Refine, sequence path
-    TextField<String> refineSequencePath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_SEQUENCE_PATH);
-    refineSequencePath.setHidden(fieldsHidden);
-    refineSequencePath.setDisabled(fieldsDisabled);
-    refineSequencePath
-      .setValue(xTandemParameterSet.getRefineSequencePath());
-    fs.add(refineSequencePath);
-    // Refine, tic percent
-    TextField<String> refineTicPercent = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_TIC_PERCENT);
-    refineTicPercent.setHidden(fieldsHidden);
-    refineTicPercent.setDisabled(fieldsDisabled);
-    refineTicPercent.setValue(xTandemParameterSet.getRefineTicPercent());
-    fs.add(refineTicPercent);
-    // Refine, spectrum synthesis
-    TextField<String> spectrumSynthesis = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_SPECTRUM_SYNTHESIS);
-    spectrumSynthesis.setHidden(fieldsHidden);
-    spectrumSynthesis.setDisabled(fieldsDisabled);
-    spectrumSynthesis.setValue(xTandemParameterSet
-      .getRefineSpectrumSynthesis());
-    fs.add(spectrumSynthesis);
-    // Refine, maximum valid expectation value
-    TextField<String> maxValidExpectationValue = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE);
-    maxValidExpectationValue.setHidden(fieldsHidden);
-    maxValidExpectationValue.setDisabled(fieldsDisabled);
-    maxValidExpectationValue.setValue(xTandemParameterSet
-      .getRefineMaximumValidExpectationValue());
-    fs.add(maxValidExpectationValue);
-    // Refine, potential N-terminus modifications
-    TextField<String> potentialNTerminusModifications = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS);
-    potentialNTerminusModifications.setHidden(fieldsHidden);
-    potentialNTerminusModifications.setDisabled(fieldsDisabled);
-    potentialNTerminusModifications.setValue(xTandemParameterSet
-      .getRefinePotentialNTerminusModifications());
-    fs.add(potentialNTerminusModifications);
-    // Refine, potential C-terminus modifications
-    TextField<String> potentialCTerminusModifications = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS);
-    potentialCTerminusModifications.setHidden(fieldsHidden);
-    potentialCTerminusModifications.setDisabled(fieldsDisabled);
-    potentialCTerminusModifications.setValue(xTandemParameterSet
-      .getRefinePotentialCTerminusModifications());
-    fs.add(potentialCTerminusModifications);
-    // Refine, unanticipated cleavage
-    TextField<String> unanticipatedCleavage = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE);
-    unanticipatedCleavage.setHidden(fieldsHidden);
-    unanticipatedCleavage.setDisabled(fieldsDisabled);
-    unanticipatedCleavage.setValue(xTandemParameterSet
-      .getRefineUnanticipatedCleavage());
-    fs.add(unanticipatedCleavage);
-    // Refine, potential modification mass
-    TextField<String> refinePotentialModificationMass = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS);
-    refinePotentialModificationMass.setHidden(fieldsHidden);
-    refinePotentialModificationMass.setDisabled(fieldsDisabled);
-    refinePotentialModificationMass.setValue(xTandemParameterSet
-      .getRefinePotentialModificationMass());
-    fs.add(refinePotentialModificationMass);
-    // Refine, point mutations
-    TextField<String> pointMutations = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POINT_MUTATIONS);
-    pointMutations.setHidden(fieldsHidden);
-    pointMutations.setDisabled(fieldsDisabled);
-    pointMutations.setValue(xTandemParameterSet.getRefinePointMutations());
-    fs.add(pointMutations);
-    // Refine, use potential modifications for full refinement
-    TextField<String> usePotentialModificationsForFullRefinement = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT);
-    usePotentialModificationsForFullRefinement.setHidden(fieldsHidden);
-    usePotentialModificationsForFullRefinement.setDisabled(fieldsDisabled);
-    usePotentialModificationsForFullRefinement.setValue(xTandemParameterSet
-      .getRefineUsePotentialModificationsForFullRefinement());
-    fs.add(usePotentialModificationsForFullRefinement);
-    // Refine, potential modification motif
-    TextField<String> potentialModificationMotifRefine = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF);
-    potentialModificationMotifRefine.setHidden(fieldsHidden);
-    potentialModificationMotifRefine.setDisabled(fieldsDisabled);
-    potentialModificationMotifRefine.setValue(xTandemParameterSet
-      .getRefinePotentialModificationMotif());
-    fs.add(potentialModificationMotifRefine);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet scoring fields to a
-   * Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetScoringFieldsToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // Scoring, minimum ion count
-    TextField<String> minIonCount = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_MIN_ION_COUNT);
-    minIonCount.setHidden(fieldsHidden);
-    minIonCount.setDisabled(fieldsDisabled);
-    minIonCount.setValue(xTandemParameterSet.getScoringMinimumIonCount());
-    fs.add(minIonCount);
-    // Scoring, maximum missed cleavage sites
-    TextField<String> maxMissedCleavageSites = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES);
-    maxMissedCleavageSites.setHidden(fieldsHidden);
-    maxMissedCleavageSites.setDisabled(fieldsDisabled);
-    maxMissedCleavageSites.setValue(xTandemParameterSet
-      .getScoringMaximumMissedCleavageSites());
-    fs.add(maxMissedCleavageSites);
-    // Scoring, x ions
-    TextField<String> xIons = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_X_IONS);
-    xIons.setHidden(fieldsHidden);
-    xIons.setDisabled(fieldsDisabled);
-    xIons.setValue(xTandemParameterSet.getScoringXIons());
-    fs.add(xIons);
-    // Scoring, y ions
-    TextField<String> yIons = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_Y_IONS);
-    yIons.setHidden(fieldsHidden);
-    yIons.setDisabled(fieldsDisabled);
-    yIons.setValue(xTandemParameterSet.getScoringYIons());
-    fs.add(yIons);
-    // Scoring, z ions
-    TextField<String> zIons = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_Z_IONS);
-    zIons.setHidden(fieldsHidden);
-    zIons.setDisabled(fieldsDisabled);
-    zIons.setValue(xTandemParameterSet.getScoringZIons());
-    fs.add(zIons);
-    // Scoring, a ions
-    TextField<String> aIons = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_A_IONS);
-    aIons.setHidden(fieldsHidden);
-    aIons.setDisabled(fieldsDisabled);
-    aIons.setValue(xTandemParameterSet.getScoringAIons());
-    fs.add(aIons);
-    // Scoring, b ions
-    TextField<String> bIons = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_B_IONS);
-    bIons.setHidden(fieldsHidden);
-    bIons.setDisabled(fieldsDisabled);
-    bIons.setValue(xTandemParameterSet.getScoringBIons());
-    fs.add(bIons);
-    // Scoring, c ions
-    TextField<String> cIons = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_C_IONS);
-    cIons.setHidden(fieldsHidden);
-    cIons.setDisabled(fieldsDisabled);
-    cIons.setValue(xTandemParameterSet.getScoringCIons());
-    fs.add(cIons);
-    // Scoring, cyclic permutation
-    TextField<String> cyclicPermutation = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_CYCLIC_PERMUTATION);
-    cyclicPermutation.setHidden(fieldsHidden);
-    cyclicPermutation.setDisabled(fieldsDisabled);
-    cyclicPermutation.setValue(xTandemParameterSet
-      .getScoringCyclicPermutation());
-    fs.add(cyclicPermutation);
-    // Scoring, include reverse
-    TextField<String> includeReverse = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_INCLUDE_REVERSE);
-    includeReverse.setHidden(fieldsHidden);
-    includeReverse.setDisabled(fieldsDisabled);
-    includeReverse.setValue(xTandemParameterSet.getScoringIncludeReverse());
-    fs.add(includeReverse);
-    // Scoring, algorithm
-    TextField<String> algorithm = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_SCORING_ALGORITHM);
-    algorithm.setHidden(fieldsHidden);
-    algorithm.setDisabled(fieldsDisabled);
-    algorithm.setValue(xTandemParameterSet.getScoringAlgorithm());
-    fs.add(algorithm);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Convenience method for adding XTandemParameterSet output fields to a
-   * Fieldset.
-   * 
-   * @param xTandemParameterSet XTandemParameterSet object (need not be stored
-   *        in database) with default field values.
-   * @param fs Fieldset The Fieldset to add the XTandemParameterSet fields to.
-   * @param fieldsHidden boolean Flag indicating that added fields should be
-   *        hidden.
-   * @param fieldsDisabled boolean Flag indicating that added fields should be
-   *        disabled.
-   * @return Fieldset The input fieldset with added XTandemParameterSet
-   *         fields.
-   */
-  public Fieldset addXTandemParameterSetOutputFieldsToFieldset(
-      XTandemParameterSet xTandemParameterSet, Fieldset fs,
-      boolean fieldsHidden, boolean fieldsDisabled)
-  {
-    // Output, path
-    TextField<String> outputPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PATH);
-    outputPath.setHidden(fieldsHidden);
-    outputPath.setDisabled(fieldsDisabled);
-    outputPath.setValue(xTandemParameterSet.getOutputPath());
-    fs.add(outputPath);
-    // Output, log path
-    TextField<String> outputLogPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_LOG_PATH);
-    outputLogPath.setHidden(fieldsHidden);
-    outputLogPath.setDisabled(fieldsDisabled);
-    outputLogPath.setValue(xTandemParameterSet.getOutputLogPath());
-    fs.add(outputLogPath);
-    // Output, message
-    TextField<String> outputMessage = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_MESSAGE);
-    outputMessage.setHidden(fieldsHidden);
-    outputMessage.setDisabled(fieldsDisabled);
-    outputMessage.setValue(xTandemParameterSet.getOutputMessage());
-    fs.add(outputMessage);
-    // Output, sequence path
-    TextField<String> outputSequencePath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SEQUENCE_PATH);
-    outputSequencePath.setHidden(fieldsHidden);
-    outputSequencePath.setDisabled(fieldsDisabled);
-    outputSequencePath
-      .setValue(xTandemParameterSet.getOutputSequencePath());
-    fs.add(outputSequencePath);
-    // Output, sort results by
-    TextField<String> outputSortResultsBy = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SORT_RESULTS_BY);
-    outputSortResultsBy.setHidden(fieldsHidden);
-    outputSortResultsBy.setDisabled(fieldsDisabled);
-    outputSortResultsBy.setValue(xTandemParameterSet
-      .getOutputSortResultsBy());
-    fs.add(outputSortResultsBy);
-    // Output, path hashing
-    TextField<String> pathHashing = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PATH_HASHING);
-    pathHashing.setHidden(fieldsHidden);
-    pathHashing.setDisabled(fieldsDisabled);
-    pathHashing.setValue(xTandemParameterSet.getOutputPathHashing());
-    fs.add(pathHashing);
-    // Output, xsl path
-    TextField<String> xslPath = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_XSL_PATH);
-    xslPath.setHidden(fieldsHidden);
-    xslPath.setDisabled(fieldsDisabled);
-    xslPath.setValue(xTandemParameterSet.getOutputXslPath());
-    fs.add(xslPath);
-    // Output, parameters
-    TextField<String> parameters = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PARAMETERS);
-    parameters.setHidden(fieldsHidden);
-    parameters.setDisabled(fieldsDisabled);
-    parameters.setValue(xTandemParameterSet.getOutputParameters());
-    fs.add(parameters);
-    // Output, performance
-    TextField<String> performance = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PERFORMANCE);
-    performance.setHidden(fieldsHidden);
-    performance.setDisabled(fieldsDisabled);
-    performance.setValue(xTandemParameterSet.getOutputPerformance());
-    fs.add(performance);
-    // Output, spectra
-    TextField<String> spectra = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SPECTRA);
-    spectra.setValue(xTandemParameterSet.getOutputSpectra());
-    spectra.setHidden(fieldsHidden);
-    spectra.setDisabled(fieldsDisabled);
-    fs.add(spectra);
-    // Output, histograms
-    TextField<String> histograms = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_HISTOGRAMS);
-    histograms.setHidden(fieldsHidden);
-    histograms.setDisabled(fieldsDisabled);
-    histograms.setValue(xTandemParameterSet.getOutputHistograms());
-    fs.add(histograms);
-    // Output, proteins
-    TextField<String> proteins = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_PROTEINS);
-    proteins.setHidden(fieldsHidden);
-    proteins.setDisabled(fieldsDisabled);
-    proteins.setValue(xTandemParameterSet.getOutputProteins());
-    fs.add(proteins);
-    // Output, sequences
-    TextField<String> sequences = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_SEQUENCES);
-    sequences.setHidden(fieldsHidden);
-    sequences.setDisabled(fieldsDisabled);
-    sequences.setValue(xTandemParameterSet.getOutputSequences());
-    fs.add(sequences);
-    // Output, one sequence copy
-    TextField<String> oneSequenceCopy = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY);
-    oneSequenceCopy.setHidden(fieldsHidden);
-    oneSequenceCopy.setDisabled(fieldsDisabled);
-    oneSequenceCopy
-      .setValue(xTandemParameterSet.getOutputOneSequenceCopy());
-    fs.add(oneSequenceCopy);
-    // Output, results
-    TextField<String> results = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_RESULTS);
-    results.setHidden(fieldsHidden);
-    results.setDisabled(fieldsDisabled);
-    results.setValue(xTandemParameterSet.getOutputResults());
-    fs.add(results);
-    // Output, maximum valid expectation value
-    TextField<String> outputMaxValidExpectationValue = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE);
-    outputMaxValidExpectationValue.setHidden(fieldsHidden);
-    outputMaxValidExpectationValue.setDisabled(fieldsDisabled);
-    outputMaxValidExpectationValue.setValue(xTandemParameterSet
-      .getOutputMaximumValidExpectationValue());
-    fs.add(outputMaxValidExpectationValue);
-    // Output, histogram column width
-    TextField<String> histogramColumnWidth = new TextField<String>(SaveXTandemParameterSetStorage.VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH);
-    histogramColumnWidth.setHidden(fieldsHidden);
-    histogramColumnWidth.setDisabled(fieldsDisabled);
-    histogramColumnWidth.setValue(xTandemParameterSet
-      .getOutputHistogramColumnWidth());
-    fs.add(histogramColumnWidth);
-    // Return Fieldset with added fields
-    return fs;
-  }
-
-
-  /**
-   * Checks if a string is found as option value in an option list.
-   * 
-   * @param optionList List<Option> Option list of options.
-   * @param item String String to look for in option values.
-   * @return boolean True if item found as option value, else false.
-   */
-  private boolean itemInOptionList(List<Option> optionList, String item)
-  {
-    boolean isFound = false;
-    // Check if item if found as option value in option list
-    if (optionList != null)
-    {
-      for (int i = 0; i < optionList.size(); i++)
-      {
-        if (optionList.get(i) != null)
-        {
-          if (optionList.get(i).getValue().equals(item))
-          {
-            isFound = true;
-            break;
-          }
-        }
-      }
-    }
-    return isFound;
-  }
-
-
-  /**
-   * Checks if all strings in input list are found as option values in an
-   * option list.
-   * 
-   * @param optionList List<Option> Option list of options.
-   * @param itemList List<String> List with strings to look for in option
-   *        values.
-   * @return boolean True if all items found as option values, else false.
-   */
-  private boolean allItemsInOptionList(List<Option> optionList,
-      List<String> itemList)
-  {
-    // Check if all items are found among option values
-    if (itemList != null)
-    {
-      for (int j = 0; j < itemList.size(); j++)
-      {
-        if (itemList.get(j) != null)
-        {
-          String item = itemList.get(j);
-          // Check if item is found among option values
-          boolean isFound = false;
-          if (optionList != null)
-          {
-            for (int i = 0; i < optionList.size(); i++)
-            {
-              if (optionList.get(i) != null)
-              {
-                if (optionList.get(i).getValue().equals(item))
-                {
-                  isFound = true;
-                }
-              }
-            }
-          }
-          // Return if item was not found among option values
-          if (!isFound)
-          {
-            log
-              .debug("j = " + j + " item = \"" + item + "\" isFound = " + isFound + " - return false");
-            return false;
-          }
-        }
-      }
-    }
-    return true;
-  }
-
-
-  /**
-   * Converts a list String to a list with String elements. If the list string
-   * contains two delimiter strings directly after each other, an empty string
-   * element will be added to the list in the corresponding place. Example:
-   * List string "one, two, three" will be converted to a list with the three
-   * String elements "one", "two", and "three" using delimiter regular
-   * expression ",\\ ".
-   * 
-   * @param listString String A string with a list
-   * @param delimiterRegex String A regular expression for the delimiter
-   *        between list elements
-   * @return List<String> A list of String elements
-   */
-  private List<String> listStringToStringList(String listString,
-      String delimiterRegex)
-  {
-    List<String> stringList = null;
-    if (listString != null)
-    {
-      stringList = new ArrayList<String>(0);
-      for (String part : listString.split(delimiterRegex, -1))
-      {
-        // Add list part if not already in list
-        if (part != null && !stringList.contains(part))
-        {
-          stringList.add(part);
-        }
-      }
-    }
-    return stringList;
-  }
-
 }

trunk/client/servlet/src/org/proteios/gui/form/Select.java

@@ -71 +71 @@
   }
 
- public Select(D param ,  List<Option> optionList, List<String> selected)
+ public Select(D param, List<Option> optionList, List<String> selected)
  {
   this(param);
-  this.options.addAll(options);
-  for(String str : selected)
-  {
-   selectOption(str);
+  this.options.addAll(optionList);
+  if (selected != null)
+  {   
+    for(String str : selected)
+    {
+      selectOption(str);
+    }
   }
   setMaxSize(5);  
@@ -174 +177 @@
   }
 
+ 
+ /**
+  * Sets all options matching any value in the input list to selected.
+  * 
+  * @param List<Sting> selected List with selected values.
+  */
+ public void selectOptions(List<String> selected)
+ {
+   if (selected != null)
+   {
+     for(String str : selected)
+     {
+       selectOption(str);
+     }
+   }
+ }
 }