Changeset 3903


Ignore:
Timestamp:
Oct 20, 2010, 3:49:00 PM (13 years ago)
Author:
olle
Message:

Refs #700. Class/file gui/form/XTandemParameterSetFormSimple.java in
client/servlet/ updated to create a simple X!Tandem search form:

  1. Valid parameters defined in class XTandemParameterSetForm used for form elements, in order to ensure that form data can be

transferred between the two classes.

  1. Public constructor XTandemParameterSetFormSimple() sets

attribute hidden to true for all form elements that should not
be visible in the simple form. Hidden fields and select boxes that
were originally placed in a field set that is now unused, are
instead added to one of the used field sets,
hiddenFieldContainerFS, which is set to the spectrum field set
in this version.

  1. Public constructor XTandemParameterSetFormSimple(XTandemParameterSet obj)

stores data for the hidden multiple-choice selection box for refine
potential modification mass in hidden text fields coupled to the same
valid parameter as the select box, since this method at present was
more successful in transferring data between forms.

File:
1 edited

Legend:

Unmodified
Added
Removed

  • trunk/client/servlet/src/org/proteios/gui/form/XTandemParameterSetFormSimple.java

    r3902 r3903  
    3939    extends Form
    4040{
    41   public static final VString VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS = new VString("XTandemListPathDefaultParameters", 0,
    42     255, false);
    43   public static final VString VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION = new VString("XTandemListPathTaxonomyInformation", 0,
    44     255, false);
    45   public static final VString VXTANDEM_SPECTRUM_PATH = new VString("XTandemSpectrumPath", 0,
    46     255, false);
    47   public static final VString VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR = new VString("XTandemSpectrumFragmentMonoisotopicMassError", 0,
    48     32, false);
    49   public static final VString VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS = new VString("XTandemSpectrumFragmentMonoisotopicMassErrorUnits", 0,
    50     32, false);
    51   public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS = new VString("XTandemSpectrumParentMonoisotopicMassErrorPlus", 0,
    52     32, false);
    53   public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS = new VString("XTandemSpectrumParentMonoisotopicMassErrorMinus", 0,
    54     32, false);
    55   public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR = new VString("XTandemSpectrumParentMonoisotopicMassIsotopeError", 0,
    56     32, false);
    57   public static final VString VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS = new VString("XTandemSpectrumParentMonoisotopicMassErrorUnits", 0,
    58     32, false);
    59   public static final VString VXTANDEM_SPECTRUM_FRAG_MASS_TYPE = new VString("XTandemSpectrumFragmentMassType", 0,
    60     32, false);
    61   public static final VString VXTANDEM_SPECTRUM_DYNAMIC_RANGE = new VString("XTandemSpectrumDynamicRange", 0,
    62     32, false);
    63   public static final VString VXTANDEM_SPECTRUM_TOTAL_PEAKS = new VString("XTandemSpectrumTotalPeaks", 0,
    64     32, false);
    65   public static final VString VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE = new VString("XTandemSpectrumMaximumParentCharge", 0,
    66     32, false);
    67   public static final VString VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION = new VString("XTandemSpectrumUseNoiseSuppression", 0,
    68     32, false);
    69   public static final VString VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H = new VString("XTandemSpectrumMinimumParentMPlusH", 0,
    70     32, false);
    71   public static final VString VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H = new VString("XTandemSpectrumMaximumParentMPlusH", 0,
    72     32, false);
    73   public static final VString VXTANDEM_SPECTRUM_MIN_FRAG_MZ = new VString("XTandemSpectrumMinimumFragmentMz", 0,
    74     32, false);
    75   public static final VString VXTANDEM_SPECTRUM_MIN_PEAKS = new VString("XTandemSpectrumMinimumPeaks", 0,
    76     32, false);
    77   public static final VString VXTANDEM_SPECTRUM_THREADS = new VString("XTandemSpectrumThreads", 0,
    78     32, false);
    79   public static final VString VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE = new VString("XTandemSpectrumSequenceBatchSize", 0,
    80     32, false);
    81   public static final VString VXTANDEM_SPECTRUM_USE_CONDITIONING = new VString("XTandemSpectrumUseConditioning", 0,
    82     32, false);
    83   public static final VString VXTANDEM_RESIDUE_MODIFICATION_MASS_SELECT = new VString("XTandemResidueModificationMassSelect", 0,
    84     32, false);
    85   public static final VString VXTANDEM_RESIDUE_MODIFICATION_MASS = new VString("XTandemResidueModificationMass", 0,
    86     150, false);
    87   public static final VString VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT = new VString("XTandemResiduePotentialModificationMassSelect", 0,
    88     32, false);
    89   public static final VString VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS = new VString("XTandemResiduePotentialModificationMass", 0,
    90     150, false);
    91   public static final VString VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF = new VString("XTandemResiduePotentialModificationMotif", 0,
    92     100, false);
    93   public static final VString VXTANDEM_PROTEIN_TAXON = new VString("XTandemProteinTaxon", 0,
    94     64, false);
    95   public static final VString VXTANDEM_PROTEIN_TAXON1 = new VString("XTandemProteinTaxon1", 0,
    96     64, false);
    97   public static final VString VXTANDEM_PROTEIN_CLEAVAGE_SITE_SELECT = new VString("XTandemProteinCleavageSiteSelect", 0,
    98     32, false);
    99   public static final VString VXTANDEM_PROTEIN_CLEAVAGE_SITE = new VString("XTandemProteinCleavageSite", 0,
    100     32, false);
    101   public static final VString VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE = new VString("XTandemProteinModifiedResidueMassFile", 0,
    102     32, false);
    103   public static final VString VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE = new VString("XTandemProteinCleavageNTerminalMassChange", 0,
    104     32, false);
    105   public static final VString VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE = new VString("XTandemProteinCleavageCTerminalMassChange", 0,
    106     32, false);
    107   public static final VString VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS = new VString("XTandemProteinNTerminalResidueModificationMass", 0,
    108     32, false);
    109   public static final VString VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS = new VString("XTandemProteinCTerminalResidueModificationMass", 0,
    110     32, false);
    111   public static final VString VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT = new VString("XTandemProteinHomologManagement", 0,
    112     32, false);
    113   public static final VString VXTANDEM_REFINE = new VString("XTandemRefine", 0,
    114     32, false);
    115   public static final VString VXTANDEM_REFINE_MODIFICATION_MASS = new VString("XTandemRefineModificationMass", 0,
    116     32, false);
    117   public static final VString VXTANDEM_REFINE_SEQUENCE_PATH = new VString("XTandemRefineSequencePath", 0,
    118     255, false);
    119   public static final VString VXTANDEM_REFINE_TIC_PERCENT = new VString("XTandemRefineTicPercent", 0,
    120     32, false);
    121   public static final VString VXTANDEM_REFINE_SPECTRUM_SYNTHESIS = new VString("XTandemRefineSpectrumSynthesis", 0,
    122     32, false);
    123   public static final VString VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE = new VString("XTandemRefineMaximumValidExpectationValue", 0,
    124     32, false);
    125   public static final VString VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS = new VString("XTandemRefinePotentialNTerminusModifications", 0,
    126     32, false);
    127   public static final VString VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS = new VString("XTandemRefinePotentialCTerminusModifications", 0,
    128     32, false);
    129   public static final VString VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE = new VString("XTandemRefineUnanticipatedCleavage", 0,
    130     32, false);
    131   public static final VString VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT = new VString("XTandemRefinePotentialModificationMassSelect", 0,
    132     32, false);
    133   public static final VString VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS = new VString("XTandemRefinePotentialModificationMass", 0,
    134     32, false);
    135   public static final VString VXTANDEM_REFINE_POINT_MUTATIONS = new VString("XTandemRefinePointMutations", 0,
    136     32, false);
    137   public static final VString VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT = new VString("XTandemRefineUsePotentialModificationsForFullRefinement", 0,
    138     32, false);
    139   public static final VString VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF = new VString("XTandemRefinePotentialModificationMotif", 0,
    140     32, false);
    141   public static final VString VXTANDEM_SCORING_MIN_ION_COUNT = new VString("XTandemScoringMinIonCount", 0,
    142     32, false);
    143   public static final VString VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES = new VString("XTandemScoringMaxMissedCleavageSites", 0,
    144     32, false);
    145   public static final VString VXTANDEM_SCORING_X_IONS = new VString("XTandemScoringXIons", 0,
    146     32, false);
    147   public static final VString VXTANDEM_SCORING_Y_IONS = new VString("XTandemScoringYIons", 0,
    148     32, false);
    149   public static final VString VXTANDEM_SCORING_Z_IONS = new VString("XTandemScoringZIons", 0,
    150     32, false);
    151   public static final VString VXTANDEM_SCORING_A_IONS = new VString("XTandemScoringAIons", 0,
    152     32, false);
    153   public static final VString VXTANDEM_SCORING_B_IONS = new VString("XTandemScoringBIons", 0,
    154     32, false);
    155   public static final VString VXTANDEM_SCORING_C_IONS = new VString("XTandemScoringCIons", 0,
    156     32, false);
    157   public static final VString VXTANDEM_SCORING_CYCLIC_PERMUTATION = new VString("XTandemScoringCyclicPermutation", 0,
    158     32, false);
    159   public static final VString VXTANDEM_SCORING_INCLUDE_REVERSE = new VString("XTandemScoringIncludeReverse", 0,
    160     32, false);
    161   public static final VString VXTANDEM_SCORING_ALGORITHM = new VString("XTandemScoringAlgorithm", 0,
    162     32, false);
    163   public static final VString VXTANDEM_OUTPUT_PATH = new VString("XTandemOutputPath", 0,
    164     255, false);
    165   public static final VString VXTANDEM_OUTPUT_LOG_PATH = new VString("XTandemOutputLogPath", 0,
    166     255, false);
    167   public static final VString VXTANDEM_OUTPUT_MESSAGE = new VString("XTandemOutputMessage", 0,
    168     255, false);
    169   public static final VString VXTANDEM_OUTPUT_SEQUENCE_PATH = new VString("XTandemOutputSequencePath", 0,
    170     255, false);
    171   public static final VString VXTANDEM_OUTPUT_SORT_RESULTS_BY = new VString("XTandemOutputSortResultsBy", 0,
    172     32, false);
    173   public static final VString VXTANDEM_OUTPUT_PATH_HASHING = new VString("XTandemOutputPathHashing", 0,
    174     255, false);
    175   public static final VString VXTANDEM_OUTPUT_XSL_PATH = new VString("XTandemOutputXslPath", 0,
    176     255, false);
    177   public static final VString VXTANDEM_OUTPUT_PARAMETERS = new VString("XTandemOutputParameters", 0,
    178     32, false);
    179   public static final VString VXTANDEM_OUTPUT_PERFORMANCE = new VString("XTandemOutputPerformance", 0,
    180     32, false);
    181   public static final VString VXTANDEM_OUTPUT_SPECTRA = new VString("XTandemOutputSpectra", 0,
    182     32, false);
    183   public static final VString VXTANDEM_OUTPUT_HISTOGRAMS = new VString("XTandemOutputHistograms", 0,
    184     32, false);
    185   public static final VString VXTANDEM_OUTPUT_PROTEINS = new VString("XTandemOutputProteins", 0,
    186     32, false);
    187   public static final VString VXTANDEM_OUTPUT_SEQUENCES = new VString("XTandemOutputSequences", 0,
    188     32, false);
    189   public static final VString VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY = new VString("XTandemOutputOneSequenceCopy", 0,
    190     32, false);
    191   public static final VString VXTANDEM_OUTPUT_RESULTS = new VString("XTandemOutputResults", 0,
    192     32, false);
    193   public static final VString VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE = new VString("XTandemOutputMaximumValidExpectationValue", 0,
    194     32, false);
    195   public static final VString VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH = new VString("XTandemOutputHistogramColumnWidth", 0,
    196     32, false);
    197  
    19841  private static final org.apache.log4j.Logger log = org.apache.log4j.LogManager
    19942    .getLogger("org.proteios.gui.form");
    … …  
    24083  public TextField<String> cTerminalResidueModificationMassF;
    24184  public Select<VString> homologManagementM;
    242   public Fieldset refineFS;
     85  //public Fieldset refineFS;
    24386  public Select<VString> refineM;
    24487  public TextField<String> refineModificationMassF;
    … …  
    267110  public Select<VString> includeReverseM;
    268111  public Select<VString> algorithmM;
    269   public Fieldset outputFS;
     112  //public Fieldset outputFS;
    270113  public TextField<String> outputPathF;
    271114  public TextField<String> outputLogPathF;
    … …  
    302145  public XTandemParameterSetFormSimple()
    303146  {
    304     setTitle("XTandemParameterSetForm");
    305     setId("XTandemParameterSetForm");
     147    setTitle("XTandemParameterSetFormSimple");
     148    setId("XTandemParameterSetFormSimple");
    306149    // Fetch lists of option alternatives
    307150    fetchOptionAlternatives();
    … …  
    332175    /*
    333176    listPathDefaultParametersSB = createSingleSelectBox(
    334       VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS,
     177      XTandemParameterSetForm.VXTANDEM_LIST_PATH_DEFAULT_PARAMETERS,
    335178      "XTandemListPathDefaultParameters",
    336179      this.listPathDefaultParametersOptionList,
    … …  
    340183    */
    341184    // List path, taxonomy information
    342     taxonomyInformationListPathF = new TextField<String>(VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION);
     185    taxonomyInformationListPathF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_LIST_PATH_TAXONOMY_INFORMATION);
    343186    //listPathFS.add(taxonomyInformationListPathF);
    344187    taxonomyInformationListPathF.setHidden(true);
    … …  
    354197    */
    355198    // Spectrum, path
    356     spectrumPathF = new TextField<String>(VXTANDEM_SPECTRUM_PATH);
     199    spectrumPathF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PATH);
     200    spectrumPathF.setHidden(true);
    357201    spectrumFS.add(spectrumPathF);
    358202    // Spectrum, fragment monoisotopic mass error
    359     fragMiMassErrorF = new TextField<String>(VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR);
     203    fragMiMassErrorF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR);
    360204    spectrumFS.add(fragMiMassErrorF);
    361205    // Spectrum, fragment monoisotopic mass error units
    362     validStringParam = VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS;
     206    validStringParam = XTandemParameterSetForm.VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS;
    363207    stringList = new ArrayList<String>();
    364208    stringList.add("Daltons");
    … …  
    367211    spectrumFS.add(fragMiMassErrorUnitsM);
    368212    // Spectrum, parent monoisotopic mass error plus
    369     parentMiMassErrorPlusF = new TextField<String>(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS);
     213    parentMiMassErrorPlusF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS);
    370214    spectrumFS.add(parentMiMassErrorPlusF);
    371215    // Spectrum, parent monoisotopic mass error minus
    372     parentMiMassErrorMinusF = new TextField<String>(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS);
     216    parentMiMassErrorMinusF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS);
    373217    spectrumFS.add(parentMiMassErrorMinusF);
    374218    // Spectrum, parent monoisotopic mass isotope error
    375     validStringParam = VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR;
     219    validStringParam = XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR;
    376220    stringList = new ArrayList<String>();
    377221    stringList.add("yes");
    378222    stringList.add("no");
    379223    parentMiMassIsotopeErrorM = new Select<VString>(validStringParam, stringList, null);
     224    parentMiMassIsotopeErrorM.setHidden(true);
    380225    spectrumFS.add(parentMiMassIsotopeErrorM);
    381226    // Spectrum, parent monoisotopic mass error units
    382     validStringParam = VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS;
     227    validStringParam = XTandemParameterSetForm.VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_UNITS;
    383228    stringList = new ArrayList<String>();
    384229    stringList.add("Daltons");
    … …  
    387232    spectrumFS.add(parentMiMassErrorUnitsM);
    388233    // Spectrum, fragment mass type
    389     validStringParam = VXTANDEM_SPECTRUM_FRAG_MASS_TYPE;
     234    validStringParam = XTandemParameterSetForm.VXTANDEM_SPECTRUM_FRAG_MASS_TYPE;
    390235    stringList = new ArrayList<String>();
    391236    stringList.add("monoisotopic");
    392237    stringList.add("average");
    393238    fragMassTypeM = new Select<VString>(validStringParam, stringList, null);
     239    fragMassTypeM.setHidden(true);
    394240    spectrumFS.add(fragMassTypeM);
    395241    // Spectrum, dynamic range
    396     dynamicRangeF = new TextField<String>(VXTANDEM_SPECTRUM_DYNAMIC_RANGE);
     242    dynamicRangeF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_DYNAMIC_RANGE);
     243    dynamicRangeF.setHidden(true);
    397244    spectrumFS.add(dynamicRangeF);
    398245    // Spectrum, total peaks
    399     totalPeaksF = new TextField<String>(VXTANDEM_SPECTRUM_TOTAL_PEAKS);
     246    totalPeaksF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_TOTAL_PEAKS);
     247    totalPeaksF.setHidden(true);
    400248    spectrumFS.add(totalPeaksF);
    401249    // Spectrum, maximum parent charge
    402     maxParentChargeF = new TextField<String>(VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE);
     250    maxParentChargeF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MAX_PARENT_CHARGE);
     251    maxParentChargeF.setHidden(true);
    403252    spectrumFS.add(maxParentChargeF);
    404253    // Spectrum, use noise suppression
    405     validStringParam = VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION;
     254    validStringParam = XTandemParameterSetForm.VXTANDEM_SPECTRUM_USE_NOISE_SUPPRESSION;
    406255    stringList = new ArrayList<String>();
    407256    stringList.add("yes");
    408257    stringList.add("no");
    409258    useNoiseSuppressionM = new Select<VString>(validStringParam, stringList, null);
     259    useNoiseSuppressionM.setHidden(true);
    410260    spectrumFS.add(useNoiseSuppressionM);
    411261    // Spectrum, minimum parent m+h
    412     minParentMPlusHF = new TextField<String>(VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H);
     262    minParentMPlusHF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MIN_PARENT_M_PLUS_H);
     263    minParentMPlusHF.setHidden(true);
    413264    spectrumFS.add(minParentMPlusHF);
    414265    // Spectrum, maximum parent m+h
    415     maxParentMPlusHF = new TextField<String>(VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H);
     266    maxParentMPlusHF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MAX_PARENT_M_PLUS_H);
     267    maxParentMPlusHF.setHidden(true);
    416268    spectrumFS.add(maxParentMPlusHF);
    417269    // Spectrum, minimum fragment mz
    418     minFragmentMzF = new TextField<String>(VXTANDEM_SPECTRUM_MIN_FRAG_MZ);
     270    minFragmentMzF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MIN_FRAG_MZ);
     271    minFragmentMzF.setHidden(true);
    419272    spectrumFS.add(minFragmentMzF);
    420273    // Spectrum, minimum peaks
    421     minPeaksF = new TextField<String>(VXTANDEM_SPECTRUM_MIN_PEAKS);
     274    minPeaksF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_MIN_PEAKS);
     275    minPeaksF.setHidden(true);
    422276    spectrumFS.add(minPeaksF);
    423277    // Spectrum, threads
    424     threadsF = new TextField<String>(VXTANDEM_SPECTRUM_THREADS);
     278    threadsF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_THREADS);
     279    threadsF.setHidden(true);
    425280    spectrumFS.add(threadsF);
    426281    // Spectrum, sequence batch size
    427     spectrumSequenceBatchSizeF = new TextField<String>(VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE);
     282    spectrumSequenceBatchSizeF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SPECTRUM_SEQUENCE_BATCH_SIZE);
     283    spectrumSequenceBatchSizeF.setHidden(true);
    428284    spectrumFS.add(spectrumSequenceBatchSizeF);
    429285    /*
    … …  
    440296     * is empty.
    441297     */
    442     validStringParam = VXTANDEM_RESIDUE_MODIFICATION_MASS_SELECT;
     298    validStringParam = XTandemParameterSetForm.VXTANDEM_RESIDUE_MODIFICATION_MASS_SELECT;
    443299    residueModificationMassM = new Select<VString>(
    444300      validStringParam, this.residueModificationMassOptionList);
    … …  
    448304    residueFS.add(residueModificationMassM);
    449305    // Residue, modification mass (own entered value)
    450     modificationMassF = new TextField<String>(VXTANDEM_RESIDUE_MODIFICATION_MASS);
     306    modificationMassF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_RESIDUE_MODIFICATION_MASS);
    451307    modificationMassF.setLabel("XTandemResidueModificationMassEnter");
    452308    residueFS.add(modificationMassF);
    … …  
    461317     */
    462318    residuePotentialModificationMassSB = createMultipleSelectBox(
    463       VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT,
     319      XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT,
    464320      "XTandemResiduePotentialModificationMassSelect",
    465321      this.residuePotentialModificationMassOptionList,
    … …  
    468324    residueFS.add(residuePotentialModificationMassSB);
    469325    // Residue, potential modification mass
    470     potentialModificationMassF = new TextField<String>(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS);
     326    potentialModificationMassF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS);
    471327    potentialModificationMassF
    472328      .setLabel("XTandemResiduePotentialModificationMassEnter");
    473329    residueFS.add(potentialModificationMassF);
    474330    // Residue, potential modification motif
    475     potentialModificationMotifF = new TextField<String>(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF);
     331    potentialModificationMotifF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF);
     332    potentialModificationMotifF.setHidden(true);
    476333    residueFS.add(potentialModificationMotifF);
    477334    /*
    … …  
    490347    // Taxon - Eukaryotes
    491348    taxonSB = createMultipleSelectBox(
    492       VXTANDEM_PROTEIN_TAXON,
     349      XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON,
    493350      "XTandemProteinTaxonEukaryotes",
    494351      this.speciesOptionList,
    … …  
    498355    // Taxon - Prokaryotes
    499356    taxon1SB = createMultipleSelectBox(
    500       VXTANDEM_PROTEIN_TAXON1,
     357      XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON1,
    501358      "XTandemProteinTaxonProkaryotes",
    502359      this.proSpeciesOptionList,
    … …  
    511368     * is empty.
    512369     */
    513     validStringParam = VXTANDEM_PROTEIN_CLEAVAGE_SITE_SELECT;
     370    validStringParam = XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_SITE_SELECT;
    514371    proteinCleavageSiteM = new Select<VString>(
    515372      validStringParam, this.proteinCleavageSiteOptionList);
    … …  
    517374      .setLabel("XTandemProteinCleavageSiteSelect");
    518375    proteinCleavageSiteM.selectOption(null);
     376    proteinCleavageSiteM.setHidden(true);
    519377    proteinFS.add(proteinCleavageSiteM);
    520378    // Protein, cleavage site (own entered value)
    521     cleavageSiteF = new TextField<String>(VXTANDEM_PROTEIN_CLEAVAGE_SITE);
     379    cleavageSiteF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_SITE);
    522380    cleavageSiteF.setLabel("XTandemProteinCleavageSiteEnter");
     381    cleavageSiteF.setHidden(true);
    523382    proteinFS.add(cleavageSiteF);
    524383    // Protein, modified residue mass file
    525     proteinModifiedResidueMassFileF = new TextField<String>(VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE);
     384    proteinModifiedResidueMassFileF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_PROTEIN_MODIFIED_RESIDUE_MASS_FILE);
     385    proteinModifiedResidueMassFileF.setHidden(true);
    526386    proteinFS.add(proteinModifiedResidueMassFileF);
    527387    // Protein, cleavage N-terminal mass change
    528     proteinCleavageNTerminalMassChangeF = new TextField<String>(VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE);
     388    proteinCleavageNTerminalMassChangeF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_N_TERMINAL_MASS_CHANGE);
     389    proteinCleavageNTerminalMassChangeF.setHidden(true);
    529390    proteinFS.add(proteinCleavageNTerminalMassChangeF);
    530391    // Protein, cleavage C-terminal mass change
    531     proteinCleavageCTerminalMassChangeF = new TextField<String>(VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE);
     392    proteinCleavageCTerminalMassChangeF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_PROTEIN_CLEAVAGE_C_TERMINAL_MASS_CHANGE);
     393    proteinCleavageCTerminalMassChangeF.setHidden(true);
    532394    proteinFS.add(proteinCleavageCTerminalMassChangeF);
    533395    // Protein, N-terminal residue modification mass
    534     nTerminalResidueModificationMassF = new TextField<String>(VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS);
     396    nTerminalResidueModificationMassF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_PROTEIN_N_TERMINAL_RESIDUE_MODIFICATION_MASS);
     397    nTerminalResidueModificationMassF.setHidden(true);
    535398    proteinFS.add(nTerminalResidueModificationMassF);
    536399    // Protein, C-terminal residue modification mass
    537     cTerminalResidueModificationMassF = new TextField<String>(VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS);
     400    cTerminalResidueModificationMassF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_PROTEIN_C_TERMINAL_RESIDUE_MODIFICATION_MASS);
     401    cTerminalResidueModificationMassF.setHidden(true);
    538402    proteinFS.add(cTerminalResidueModificationMassF);
    539403    // Protein, homolog management
    540     validStringParam = VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT;
     404    validStringParam = XTandemParameterSetForm.VXTANDEM_PROTEIN_HOMOLOG_MANAGEMENT;
    541405    stringList = new ArrayList<String>();
    542406    stringList.add("yes");
    543407    stringList.add("no");
    544408    homologManagementM = new Select<VString>(validStringParam, stringList, null);
     409    homologManagementM.setHidden(true);
    545410    proteinFS.add(homologManagementM);
    546411    /*
    547412     * Refine field set
    548413     */
     414    /*
    549415    refineFS = new Fieldset();
    550416    refineFS.setTitle("XTandemParameterSetRefine");
    551417    addFieldset(refineFS);
     418    */
    552419    // Refine
    553     validStringParam = VXTANDEM_REFINE;
     420    validStringParam = XTandemParameterSetForm.VXTANDEM_REFINE;
    554421    stringList = new ArrayList<String>();
    555422    stringList.add("yes");
    556423    stringList.add("no");
    557424    refineM = new Select<VString>(validStringParam, stringList, null);
    558     refineFS.add(refineM);
     425    refineM.setHidden(true);
     426    //refineFS.add(refineM);
     427    hiddenFieldContainerFS.add(refineM);
    559428    // Refine, modification mass
    560     refineModificationMassF = new TextField<String>(VXTANDEM_REFINE_MODIFICATION_MASS);
    561     refineFS.add(refineModificationMassF);
     429    refineModificationMassF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_MODIFICATION_MASS);
     430    refineModificationMassF.setHidden(true);
     431    //refineFS.add(refineModificationMassF);
     432    hiddenFieldContainerFS.add(refineModificationMassF);
    562433    // Refine, sequence path
    563     refineSequencePathF = new TextField<String>(VXTANDEM_REFINE_SEQUENCE_PATH);
    564     refineFS.add(refineSequencePathF);
     434    refineSequencePathF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_SEQUENCE_PATH);
     435    refineSequencePathF.setHidden(true);
     436    //refineFS.add(refineSequencePathF);
     437    hiddenFieldContainerFS.add(refineSequencePathF);
    565438    // Refine, tic percent
    566     refineTicPercentF = new TextField<String>(VXTANDEM_REFINE_TIC_PERCENT);
    567     refineFS.add(refineTicPercentF);
     439    refineTicPercentF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_TIC_PERCENT);
     440    refineTicPercentF.setHidden(true);
     441    //refineFS.add(refineTicPercentF);
     442    hiddenFieldContainerFS.add(refineTicPercentF);
    568443    // Refine, spectrum synthesis
    569     validStringParam = VXTANDEM_REFINE_SPECTRUM_SYNTHESIS;
     444    validStringParam = XTandemParameterSetForm.VXTANDEM_REFINE_SPECTRUM_SYNTHESIS;
    570445    stringList = new ArrayList<String>();
    571446    stringList.add("yes");
    572447    stringList.add("no");
    573448    spectrumSynthesisM = new Select<VString>(validStringParam, stringList, null);
    574     refineFS.add(spectrumSynthesisM);
     449    spectrumSynthesisM.setHidden(true);
     450    //refineFS.add(spectrumSynthesisM);
     451    hiddenFieldContainerFS.add(spectrumSynthesisM);   
    575452    // Refine, maximum valid expectation value
    576     maxValidExpectationValueF = new TextField<String>(VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE);
    577     refineFS.add(maxValidExpectationValueF);
     453    maxValidExpectationValueF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_MAX_VALID_EXPECTATION_VALUE);
     454    maxValidExpectationValueF.setHidden(true);
     455    //refineFS.add(maxValidExpectationValueF);
     456    hiddenFieldContainerFS.add(maxValidExpectationValueF);
    578457    // Refine, potential N-terminus modifications
    579     potentialNTerminusModificationsF = new TextField<String>(VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS);
    580     refineFS.add(potentialNTerminusModificationsF);
     458    potentialNTerminusModificationsF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_N_TERMINUS_MODIFICATIONS);
     459    potentialNTerminusModificationsF.setHidden(true);
     460    //refineFS.add(potentialNTerminusModificationsF);
     461    hiddenFieldContainerFS.add(potentialNTerminusModificationsF);
    581462    // Refine, potential C-terminus modifications
    582     potentialCTerminusModificationsF = new TextField<String>(VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS);
    583     refineFS.add(potentialCTerminusModificationsF);
     463    potentialCTerminusModificationsF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_C_TERMINUS_MODIFICATIONS);
     464    potentialCTerminusModificationsF.setHidden(true);
     465    //refineFS.add(potentialCTerminusModificationsF);
     466    hiddenFieldContainerFS.add(potentialCTerminusModificationsF);
    584467    // Refine, unanticipated cleavage
    585     validStringParam = VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE;
     468    validStringParam = XTandemParameterSetForm.VXTANDEM_REFINE_UNANTICIPATED_CLEAVAGE;
    586469    stringList = new ArrayList<String>();
    587470    stringList.add("yes");
    588471    stringList.add("no");
    589472    unanticipatedCleavageM = new Select<VString>(validStringParam, stringList, null);
    590     refineFS.add(unanticipatedCleavageM);
     473    unanticipatedCleavageM.setHidden(true);
     474    //refineFS.add(unanticipatedCleavageM);
     475    hiddenFieldContainerFS.add(unanticipatedCleavageM);
    591476    // Refine, potential modification mass select
    592477    /*
    … …  
    599484     */
    600485    refinePotentialModificationMassSB = createMultipleSelectBox(
    601       VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT,
     486      XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT,
    602487      "XTandemRefinePotentialModificationMassSelect",
    603488      this.refinePotentialModificationMassOptionList,
    604489      4,
    605490      null);
    606     refineFS.add(refinePotentialModificationMassSB);
     491    refinePotentialModificationMassSB.setHidden(true);
     492    //refineFS.add(refinePotentialModificationMassSB);
     493    hiddenFieldContainerFS.add(refinePotentialModificationMassSB);
    607494    // Refine, potential modification mass
    608     refinePotentialModificationMassF = new TextField<String>(VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS);
     495    refinePotentialModificationMassF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS);
    609496    refinePotentialModificationMassF
    610497      .setLabel("XTandemRefinePotentialModificationMassEnter");
    611     refineFS.add(refinePotentialModificationMassF);
     498    refinePotentialModificationMassF.setHidden(true);
     499    //refineFS.add(refinePotentialModificationMassF);
     500    hiddenFieldContainerFS.add(refinePotentialModificationMassF);
    612501    // Refine, point mutations
    613     validStringParam = VXTANDEM_REFINE_POINT_MUTATIONS;
     502    validStringParam = XTandemParameterSetForm.VXTANDEM_REFINE_POINT_MUTATIONS;
    614503    stringList = new ArrayList<String>();
    615504    stringList.add("yes");
    616505    stringList.add("no");
    617506    pointMutationsM = new Select<VString>(validStringParam, stringList, null);
    618     refineFS.add(pointMutationsM);
     507    pointMutationsM.setHidden(true);
     508    //refineFS.add(pointMutationsM);
     509    hiddenFieldContainerFS.add(pointMutationsM);
    619510    // Refine, use potential modifications for full refinement
    620     validStringParam = VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT;
     511    validStringParam = XTandemParameterSetForm.VXTANDEM_REFINE_USE_POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT;
    621512    stringList = new ArrayList<String>();
    622513    stringList.add("yes");
    623514    stringList.add("no");
    624515    usePotentialModificationsForFullRefinementM = new Select<VString>(validStringParam, stringList, null);
    625     refineFS.add(usePotentialModificationsForFullRefinementM);
     516    usePotentialModificationsForFullRefinementM.setHidden(true);
     517    //refineFS.add(usePotentialModificationsForFullRefinementM);
     518    hiddenFieldContainerFS.add(usePotentialModificationsForFullRefinementM);
    626519    // Refine, potential modification motif
    627     potentialModificationMotifRefineF = new TextField<String>(VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF);
    628     refineFS.add(potentialModificationMotifRefineF);
     520    potentialModificationMotifRefineF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MOTIF);
     521    potentialModificationMotifRefineF.setHidden(true);
     522    //refineFS.add(potentialModificationMotifRefineF);
     523    hiddenFieldContainerFS.add(potentialModificationMotifRefineF);
    629524    /*
    630525     * Scoring field set
    … …  
    634529    addFieldset(scoringFS);
    635530    // Scoring, minimum ion count
    636     minIonCountF = new TextField<String>(VXTANDEM_SCORING_MIN_ION_COUNT);
     531    minIonCountF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SCORING_MIN_ION_COUNT);
     532    minIonCountF.setHidden(true);
    637533    scoringFS.add(minIonCountF);
    638534    // Scoring, maximum missed cleavage sites
    639     maxMissedCleavageSitesF = new TextField<String>(VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES);
     535    maxMissedCleavageSitesF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_SCORING_MAX_MISSED_CLEAVAGE_SITES);
     536    maxMissedCleavageSitesF.setHidden(true);
    640537    scoringFS.add(maxMissedCleavageSitesF);
    641538    // Scoring, x ions
    642     validStringParam = VXTANDEM_SCORING_X_IONS;
     539    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_X_IONS;
    643540    stringList = new ArrayList<String>();
    644541    stringList.add("yes");
    645542    stringList.add("no");
    646543    xIonsM = new Select<VString>(validStringParam,  stringList, null);
     544    xIonsM.setHidden(true);
    647545    scoringFS.add(xIonsM);
    648546    // Scoring, y ions
    649     validStringParam = VXTANDEM_SCORING_Y_IONS;
     547    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_Y_IONS;
    650548    stringList = new ArrayList<String>();
    651549    stringList.add("yes");
    652550    stringList.add("no");
    653551    yIonsM = new Select<VString>(validStringParam,  stringList, null);
     552    yIonsM.setHidden(true);
    654553    scoringFS.add(yIonsM);
    655554    // Scoring, z ions
    656     validStringParam = VXTANDEM_SCORING_Z_IONS;
     555    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_Z_IONS;
    657556    stringList = new ArrayList<String>();
    658557    stringList.add("yes");
    659558    stringList.add("no");
    660559    zIonsM = new Select<VString>(validStringParam,  stringList, null);
     560    zIonsM.setHidden(true);
    661561    scoringFS.add(zIonsM);
    662562    // Scoring, a ions
    663     validStringParam = VXTANDEM_SCORING_A_IONS;
     563    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_A_IONS;
    664564    stringList = new ArrayList<String>();
    665565    stringList.add("yes");
    666566    stringList.add("no");
    667567    aIonsM = new Select<VString>(validStringParam,  stringList, null);
     568    aIonsM.setHidden(true);
    668569    scoringFS.add(aIonsM);
    669570    // Scoring, b ions
    670     validStringParam = VXTANDEM_SCORING_B_IONS;
     571    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_B_IONS;
    671572    stringList = new ArrayList<String>();
    672573    stringList.add("yes");
    673574    stringList.add("no");
    674575    bIonsM = new Select<VString>(validStringParam,  stringList, null);
     576    bIonsM.setHidden(true);
    675577    scoringFS.add(bIonsM);
    676578    // Scoring, c ions
    677     validStringParam = VXTANDEM_SCORING_C_IONS;
     579    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_C_IONS;
    678580    stringList = new ArrayList<String>();
    679581    stringList.add("yes");
    680582    stringList.add("no");
    681583    cIonsM = new Select<VString>(validStringParam,  stringList, null);
     584    cIonsM.setHidden(true);
    682585    scoringFS.add(cIonsM);
    683586    // Scoring, cyclic permutation
    684     validStringParam = VXTANDEM_SCORING_CYCLIC_PERMUTATION;
     587    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_CYCLIC_PERMUTATION;
    685588    stringList = new ArrayList<String>();
    686589    stringList.add("yes");
    687590    stringList.add("no");
    688591    cyclicPermutationM = new Select<VString>(validStringParam, stringList, null);
     592    cyclicPermutationM.setHidden(true);
    689593    scoringFS.add(cyclicPermutationM);
    690594    // Scoring, include reverse
    691     validStringParam = VXTANDEM_SCORING_INCLUDE_REVERSE;
     595    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_INCLUDE_REVERSE;
    692596    stringList = new ArrayList<String>();
    693597    stringList.add("yes");
    694598    stringList.add("no");
    695599    includeReverseM = new Select<VString>(validStringParam, stringList, null);
     600    includeReverseM.setHidden(true);
    696601    scoringFS.add(includeReverseM);
    697602    // Scoring, algorithm
    698     validStringParam = VXTANDEM_SCORING_ALGORITHM;
     603    validStringParam = XTandemParameterSetForm.VXTANDEM_SCORING_ALGORITHM;
    699604    List<Option> optionList = new ArrayList<Option>();
    700605    optionList.add(new Option("", "native"));
    … …  
    706611     * Output field set
    707612     */
     613    /*
    708614    outputFS = new Fieldset();
    709615    outputFS.setTitle("XTandemParameterSetOutput");
    710616    addFieldset(outputFS);
     617    */
    711618    // Output, path
    712     outputPathF = new TextField<String>(VXTANDEM_OUTPUT_PATH);
    713     outputFS.add(outputPathF);
     619    outputPathF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_OUTPUT_PATH);
     620    outputPathF.setHidden(true);
     621    //outputFS.add(outputPathF);
     622    hiddenFieldContainerFS.add(outputPathF);
    714623    // Output, log path
    715     outputLogPathF = new TextField<String>(VXTANDEM_OUTPUT_LOG_PATH);
    716     outputFS.add(outputLogPathF);
     624    outputLogPathF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_OUTPUT_LOG_PATH);
     625    outputLogPathF.setHidden(true);
     626    //outputFS.add(outputLogPathF);
     627    hiddenFieldContainerFS.add(outputLogPathF);
    717628    // Output, message
    718     outputMessageF = new TextField<String>(VXTANDEM_OUTPUT_MESSAGE);
    719     outputFS.add(outputMessageF);
     629    outputMessageF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_OUTPUT_MESSAGE);
     630    outputMessageF.setHidden(true);
     631    //outputFS.add(outputMessageF);
     632    hiddenFieldContainerFS.add(outputMessageF);
    720633    // Output, sequence path
    721     outputSequencePathF = new TextField<String>(VXTANDEM_OUTPUT_SEQUENCE_PATH);
    722     outputFS.add(outputSequencePathF);
     634    outputSequencePathF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_OUTPUT_SEQUENCE_PATH);
     635    outputSequencePathF.setHidden(true);
     636    //outputFS.add(outputSequencePathF);
     637    hiddenFieldContainerFS.add(outputSequencePathF);
    723638    // Output, sort results by
    724     validStringParam = VXTANDEM_OUTPUT_SORT_RESULTS_BY;
     639    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_SORT_RESULTS_BY;
    725640    stringList = new ArrayList<String>();
    726641    stringList.add("protein");
    727642    stringList.add("spectrum");
    728643    outputSortResultsByM = new Select<VString>(validStringParam, stringList, null);
    729     outputFS.add(outputSortResultsByM);
     644    outputSortResultsByM.setHidden(true);
     645    //outputFS.add(outputSortResultsByM);
     646    hiddenFieldContainerFS.add(outputSortResultsByM);
    730647    // Output, path hashing
    731     validStringParam = VXTANDEM_OUTPUT_PATH_HASHING;
     648    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_PATH_HASHING;
    732649    stringList = new ArrayList<String>();
    733650    stringList.add("yes");
    734651    stringList.add("no");
    735652    pathHashingM = new Select<VString>(validStringParam,  stringList, null);
    736     outputFS.add(pathHashingM);
     653    pathHashingM.setHidden(true);
     654    //outputFS.add(pathHashingM);
     655    hiddenFieldContainerFS.add(pathHashingM);
    737656    // Output, xsl path
    738     xslPathF = new TextField<String>(VXTANDEM_OUTPUT_XSL_PATH);
    739     outputFS.add(xslPathF);
     657    xslPathF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_OUTPUT_XSL_PATH);
     658    xslPathF.setHidden(true);
     659    //outputFS.add(xslPathF);
     660    hiddenFieldContainerFS.add(xslPathF);
    740661    // Output, parameters
    741     validStringParam = VXTANDEM_OUTPUT_PARAMETERS;
     662    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_PARAMETERS;
    742663    stringList = new ArrayList<String>();
    743664    stringList.add("yes");
    744665    stringList.add("no");
    745666    parametersM = new Select<VString>(validStringParam, stringList, null);
    746     outputFS.add(parametersM);
     667    parametersM.setHidden(true);
     668    //outputFS.add(parametersM);
     669    hiddenFieldContainerFS.add(parametersM);
    747670    // Output, performance
    748     validStringParam = VXTANDEM_OUTPUT_PERFORMANCE;
    749     stringList = new ArrayList<String>();
    750     stringList.add("yes");
    751     stringList.add("no");
    752     performanceM = new Select<VString>(validStringParam,  stringList, null);
    753     outputFS.add(performanceM);
     671    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_PERFORMANCE;
     672    stringList = new ArrayList<String>();
     673    stringList.add("yes");
     674    stringList.add("no");
     675    performanceM = new Select<VString>(validStringParam, stringList, null);
     676    performanceM.setHidden(true);
     677    //outputFS.add(performanceM);
     678    hiddenFieldContainerFS.add(performanceM);
    754679    // Output, spectra
    755     validStringParam = VXTANDEM_OUTPUT_SPECTRA;
    756     stringList = new ArrayList<String>();
    757     stringList.add("yes");
    758     stringList.add("no");
    759     spectraM = new Select<VString>(validStringParam,  stringList, null);
    760     outputFS.add(spectraM);
     680    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_SPECTRA;
     681    stringList = new ArrayList<String>();
     682    stringList.add("yes");
     683    stringList.add("no");
     684    spectraM = new Select<VString>(validStringParam, stringList, null);
     685    spectraM.setHidden(true);
     686    //outputFS.add(spectraM);
     687    hiddenFieldContainerFS.add(spectraM);
    761688    // Output, histograms
    762     validStringParam = VXTANDEM_OUTPUT_HISTOGRAMS;
     689    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_HISTOGRAMS;
    763690    stringList = new ArrayList<String>();
    764691    stringList.add("yes");
    765692    stringList.add("no");
    766693    histogramsM = new Select<VString>(validStringParam, stringList, null);
    767     outputFS.add(histogramsM);
     694    histogramsM.setHidden(true);
     695    //outputFS.add(histogramsM);
     696    hiddenFieldContainerFS.add(histogramsM);
    768697    // Output, proteins
    769     validStringParam = VXTANDEM_OUTPUT_PROTEINS;
     698    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_PROTEINS;
    770699    stringList = new ArrayList<String>();
    771700    stringList.add("yes");
    772701    stringList.add("no");
    773702    proteinsM = new Select<VString>(validStringParam, stringList, null);
    774     outputFS.add(proteinsM);
     703    proteinsM.setHidden(true);
     704    //outputFS.add(proteinsM);
     705    hiddenFieldContainerFS.add(proteinsM);
    775706    // Output, sequences
    776     validStringParam = VXTANDEM_OUTPUT_SEQUENCES;
    777     stringList = new ArrayList<String>();
    778     stringList.add("yes");
    779     stringList.add("no");
    780     sequencesM = new Select<VString>(validStringParam,  stringList, null);
    781     outputFS.add(sequencesM);
     707    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_SEQUENCES;
     708    stringList = new ArrayList<String>();
     709    stringList.add("yes");
     710    stringList.add("no");
     711    sequencesM = new Select<VString>(validStringParam, stringList, null);
     712    sequencesM.setHidden(true);
     713    //outputFS.add(sequencesM);
     714    hiddenFieldContainerFS.add(sequencesM);
    782715    // Output, one sequence copy
    783     validStringParam = VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY;
    784     stringList = new ArrayList<String>();
    785     stringList.add("yes");
    786     stringList.add("no");
    787     oneSequenceCopyM = new Select<VString>(validStringParam,  stringList, null);
    788     outputFS.add(oneSequenceCopyM);
     716    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_ONE_SEQUENCE_COPY;
     717    stringList = new ArrayList<String>();
     718    stringList.add("yes");
     719    stringList.add("no");
     720    oneSequenceCopyM = new Select<VString>(validStringParam, stringList, null);
     721    oneSequenceCopyM.setHidden(true);
     722    //outputFS.add(oneSequenceCopyM);
     723    hiddenFieldContainerFS.add(oneSequenceCopyM);
    789724    // Output, results
    790     validStringParam = VXTANDEM_OUTPUT_RESULTS;
     725    validStringParam = XTandemParameterSetForm.VXTANDEM_OUTPUT_RESULTS;
    791726    stringList = new ArrayList<String>();
    792727    stringList.add("all");
    … …  
    794729    stringList.add("stochastic");
    795730    resultsM = new Select<VString>(validStringParam,  stringList, null);
    796     outputFS.add(resultsM);
     731    resultsM.setHidden(true);
     732    //outputFS.add(resultsM);
     733    hiddenFieldContainerFS.add(resultsM);
    797734    // Output, maximum valid expectation value
    798     outputMaxValidExpectationValueF = new TextField<String>(VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE);
    799     outputFS.add(outputMaxValidExpectationValueF);
     735    outputMaxValidExpectationValueF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_OUTPUT_MAX_VALID_EXPECTATION_VALUE);
     736    outputMaxValidExpectationValueF.setHidden(true);
     737    //outputFS.add(outputMaxValidExpectationValueF);
     738    hiddenFieldContainerFS.add(outputMaxValidExpectationValueF);
    800739    // Output, histogram column width
    801     histogramColumnWidthF = new TextField<String>(VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH);
    802     outputFS.add(histogramColumnWidthF);
     740    histogramColumnWidthF = new TextField<String>(XTandemParameterSetForm.VXTANDEM_OUTPUT_HISTOGRAM_COLUMN_WIDTH);
     741    histogramColumnWidthF.setHidden(true);
     742    //outputFS.add(histogramColumnWidthF);
     743    hiddenFieldContainerFS.add(histogramColumnWidthF);
    803744  }
    804745
    … …  
    991932    selectedList = xTandemParameterSetOptionsHelper.listStringToStringList(obj.getRefinePotentialModificationMass(), ",");
    992933    log.debug("refine potential modification mass selectedList = " + selectedList);
    993     refinePotentialModificationMassSB.selectOptions(selectedList);
     934    //refinePotentialModificationMassSB.selectOptions(selectedList);
     935    if (selectedList != null)
     936    {
     937      for (String value: selectedList)
     938      {
     939        TextField<String> field = new TextField<String>(XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
     940        field.setValue(value);
     941        field.setHidden(true);
     942        hiddenFieldContainerFS.add(field);
     943      }
     944    }
    994945    // Refine, potential modification mass
    995946    // Only insert selected values if not all found in select box
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