Changeset 3852

Timestamp:

Sep 15, 2010, 1:39:24 PM (13 years ago)

Author:

Gregory Vincic

Message:

Refs #698. Removing remaining debug log messages from FormFactory.

File:

• trunk/client/servlet/src/org/proteios/gui/form/FormFactory.java (modified) (80 diffs)

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

@@ -735 +735 @@
   private Select<VInteger> getNotificationModeSelectBox(int modeValue)
   {
-    log.debug("modeValue = " + modeValue);
     Select<VInteger> modeS = new Select<VInteger>(
       SavePreferences.VNOTIFICATIONMODE);
@@ -801 +800 @@
   private Select<VInteger> getTablePreferencesModeSelectBox(int modeValue)
   {
-    log.debug("modeValue = " + modeValue);
     Select<VInteger> modeS = new Select<VInteger>(
       SavePreferences.VTABLEPREFERENCESMODE);
@@ -1271 +1269 @@
         timeInMinutesStr = retentionTimeInMinutes.toString();
       }
-      log.debug("retentionTimeInMinutes = " + retentionTimeInMinutes);
     }
     addTableRow(propertiesTable, "RetentionTimeInMinutes",
@@ -2216 +2213 @@
       List<String> localSampleIdList = Hit.getUniqueLocalSampleIds(
         project, dc);
-      log.debug("localSampleIdList = " + localSampleIdList);
       // Check if valid local sample id values exist
       boolean validValuesExist = false;
       if (localSampleIdList != null)
       {
-        log.debug("localSampleIdList.size() = " + localSampleIdList
-          .size());
         for (int i = 0; i < localSampleIdList.size(); i++)
         {
@@ -2282 +2276 @@
     {
       List<String> fractionIdList = Hit.getUniqueFractionIds(project, dc);
-      log.debug("fractionIdList = " + fractionIdList);
       // Check if valid fraction id values exist
       boolean validValuesExist = false;
       if (fractionIdList != null)
       {
-        log.debug("fractionIdList.size() = " + fractionIdList.size());
         for (int i = 0; i < fractionIdList.size(); i++)
         {
-          log
-            .debug("fractionIdList.get(" + i + ") = " + fractionIdList
-              .get(i));
           // Get fraction id
           String fractionId = fractionIdList.get(i);
@@ -2497 +2486 @@
     List<String> scoreTypeList1 = Hit.getUniqueScoreTypes(project1, dc);
     List<String> scoreTypeList2 = Hit.getUniqueScoreTypes(project2, dc);
-    log.debug("scoreTypeList1 = " + scoreTypeList1);
-    log.debug("scoreTypeList2 = " + scoreTypeList2);
     // Combine score type lists
     List<String> scoreTypeList = new ArrayList<String>(0);
@@ -2528 +2515 @@
       }
     }
-    log.debug("scoreTypeList = " + scoreTypeList);
     // Add score type settings select boxes
     validStringParam = HitsComparisonReport.VHITSCOMPARISONSCORETYPE;
@@ -2824 +2810 @@
   private boolean itemInOptionList(List<Option> optionList, String item)
   {
-    log.debug("item = \"" + item + "\"");
     boolean isFound = false;
     // Check if item if found as option value in option list
@@ -2841 +2826 @@
       }
     }
-    log.debug("End - return " + isFound);
     return isFound;
   }
@@ -2858 +2842 @@
       List<String> itemList)
   {
-    log.debug("itemList = " + itemList);
     // Check if all items are found among option values
     if (itemList != null)
@@ -2892 +2875 @@
       }
     }
-    log.debug("End - return true");
     return true;
   }
@@ -3431 +3413 @@
     // Make sure that search type is one of "MIS" (default), "SQ", "PMF"
     String searchTypeInput = mascotParameterSet.getSearchType();
-    log.debug("(1) searchTypeInput = " + searchTypeInput);
     if (searchTypeInput == null)
     {
@@ -3441 +3422 @@
       searchTypeInput = new String("MIS");
     }
-    log.debug("(2) searchTypeInput = " + searchTypeInput);
     // Get field set legend title
     String generalFSTitle = new String("MascotParameterSetGeneral");
@@ -3456 +3436 @@
       generalFSTitle = new String("MascotParameterSetGeneralPMF");
     }
-    log.debug("generalFSTitle = " + generalFSTitle);
+    
     generalFS.setTitle(generalFSTitle);
     form.addFieldset(generalFS);
@@ -3486 +3466 @@
     {
       optionList = sequenceLibraryOptionList;
-      log.debug("Input sequence library option list used");
     }
     selected = mascotParameterSet.getDb();
-    log.debug("sequence library selected = \"" + selected + "\"");
     Select<VString> sequenceLibrarySelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -3507 +3485 @@
     {
       optionList = speciesOptionList;
-      log.debug("Input species option list used");
     }
     selected = mascotParameterSet.getSpecies();
-    log.debug("species selected = \"" + selected + "\"");
     Select<VString> speciesSelectBox = newStringSelectBox2(validStringParam, optionList, selected);
     speciesSelectBox.setLabel("MascotSpecies");
@@ -3527 +3503 @@
     {
       optionList = enzymeOptionList;
-      log.debug("Input enzyme option list used");
     }
     selected = mascotParameterSet.getEnzyme();
@@ -3546 +3521 @@
     {
       optionList = missedCleavagesOptionList;
-      log.debug("Input missed cleavages option list used");
     }
     selected = mascotParameterSet.getMissedCleavages();
-    log.debug("missed cleavages selected = \"" + selected + "\"");
     Select<VString> missedCleavagesSelectBox = newStringSelectBox2(validStringParam, optionList, selected);
     missedCleavagesSelectBox.setLabel("MascotMissedCleavagesSelect");
@@ -3565 +3538 @@
     {
       optionList = fixedModsOptionList;
-      log.debug("Input fixed mods option list used");
     }
     selected = mascotParameterSet.getFixed();
     selectedList = listStringToStringList(selected, delimRegex);
-    log.debug("fixed mods selectedList = " + selectedList);
     Select<VString> fixedMods = newStringMultipleSelectBox(validStringParam, optionList, selectedList);
     fixedMods.setLabel("MascotFixedMods");
@@ -3587 +3558 @@
     {
       optionList = variableModsOptionList;
-      log.debug("Input variable mods option list used");
     }
     selected = mascotParameterSet.getVariable();
     selectedList = listStringToStringList(selected, delimRegex);
-    log.debug("variable mods selectedList = " + selectedList);
     Select<VString> variableMods = newStringMultipleSelectBox(
       validStringParam, optionList, selectedList);
@@ -3611 +3580 @@
       {
         optionList = quantitationOptionList;
-        log.debug("Input quantitation option list used");
       }
       selected = mascotParameterSet.getQuantitation();
-      log.debug("quantitation selected = \"" + selected + "\"");
       Select<VString> quantitationSelectBox = newStringSelectBox2(validStringParam, optionList, selected);
       quantitationSelectBox.setLabel("MascotQuantitationSelect");
@@ -3643 +3610 @@
     {
       optionList = peptideTolUnitOptionList;
-      log.debug("Input peptide tolerance unit option list used");
     }
     selected = mascotParameterSet.getPepTolUnit();
-    log.debug("peptide tolerance unit selected = \"" + selected + "\"");
     Select<VString> peptideTolUnitSelectBox = newStringSelectBox2(validStringParam, optionList, selected);
     peptideTolUnitSelectBox.setLabel("MascotPeptideToleranceUnitSelect");
@@ -3665 +3630 @@
       {
         optionList = peptideIsotopeErrorOptionList;
-        log.debug("Input peptide isotope error option list used");
       }
       selected = mascotParameterSet.getPeptideIsotopeError();
-      log.debug("peptide isotope error selected = \"" + selected + "\"");
       Select<VString> peptideIsotopeErrorSelectBox = newStringSelectBox2(
         validStringParam, optionList, selected);
@@ -3692 +3655 @@
       {
         optionList = msMsTolUnitOptionList;
-        log.debug("Input MS/MS tolerance unit option list used");
       }
       selected = mascotParameterSet.getMsMsTolUnit();
-      log.debug("MS/MS tolerance unit selected = \"" + selected + "\"");
       Select<VString> msMsTolUnitSelectBox = newStringSelectBox2(
         validStringParam, optionList, selected);
@@ -3713 +3674 @@
       {
         optionList = peptideChargeOptionList;
-        log.debug("Input peptide charge option list used");
-      }
-      else
-      {
-        log.debug("Default peptide charge option list used");
       }
       selected = mascotParameterSet.getPeptideCharge();
-      log.debug("Peptide charge selected = \"" + selected + "\"");
       Select<VString> peptideChargeSelectBox = newStringSelectBox2(
         validStringParam, optionList, selected);
@@ -3737 +3692 @@
       }
       selected = mascotParameterSet.getMassIonType();
-      log.debug("Mass ion type selected = \"" + selected + "\"");
       Select<VString> massIonTypeSelectBox = newStringSelectBox2(
         validStringParam, optionList, selected);
@@ -3752 +3706 @@
     }
     selected = mascotParameterSet.getMassType();
-    log.debug("Mass type selected = \"" + selected + "\"");
     Select<VString> massTypeSelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -3770 +3723 @@
       {
         optionList = dataFormatOptionList;
-        log.debug("Input data format option list used");
       }
       selected = mascotParameterSet.getDataFormat();
-      log.debug("Data format selected = \"" + selected + "\"");
       Select<VString> dataFormatSelectBox = newStringSelectBox2(
         validStringParam, optionList, selected);
@@ -3807 +3758 @@
       {
         optionList = instrumentOptionList;
-        log.debug("Input instrument option list used");
       }
       selected = mascotParameterSet.getInstrument();
-      log.debug("Instrument selected = \"" + selected + "\"");
       Select<VString> instrumentSelectBox = newStringSelectBox2(validStringParam, optionList, selected);
       instrumentSelectBox.setLabel("MascotInstrumentSelect");
@@ -3823 +3772 @@
       errorTolerantCB.setValue("1");
       selected = mascotParameterSet.getErrorTolerant();
-      log.debug("Error tolerant selected = \"" + selected + "\"");
       errorTolerantCB.isChecked(false);
       if (selected != null && selected.equals("1"))
@@ -3837 +3785 @@
     decoyCB.setValue("1");
     selected = mascotParameterSet.getDecoy();
-    log.debug("Decoy selected = \"" + selected + "\"");
     decoyCB.isChecked(false);
     if (selected != null && selected.equals("1"))
@@ -3855 +3802 @@
     {
       optionList = reportTopOptionList;
-      log.debug("Input report top option list used");
     }
     selected = mascotParameterSet.getReportTop();
-    log.debug("Report top selected = \"" + selected + "\"");
     Select<VString> reportTopSelectBox = newStringSelectBox2(validStringParam, optionList, selected);
     reportTopSelectBox.setLabel("MascotReportTopSelect");
@@ -4358 +4303 @@
     }
     // Use input enzyme option list if present
-    if (enzymeOptionList != null)
-    {
-      log.debug("Input enzyme option list size = " + enzymeOptionList
-        .size() + " optionList.size() = " + optionList.size());
-    }
-    else
-    {
-      log
-        .debug("Input enzyme option list = null optionList.size() = " + optionList
-          .size());
-    }
     if (enzymeOptionList != null && enzymeOptionList.size() >= optionList
       .size())
     {
       optionList = enzymeOptionList;
-      log.debug("Input enzyme option list used");
-    }
-    else
-    {
-      log.debug("Default enzyme option list used");
     }
     selected = omssaParameterSet.getEnzyme();
-    log.debug("enzyme selected = \"" + selected + "\"");
-    // selectedList = listStringToStringList(selected, delimRegex);
-    // log.debug("enzyme selectedList = " + selectedList);
     Select<VString> enzymeSelectBox = newStringSelectBox2(validStringParam,
       optionList, selected);
@@ -4397 +4323 @@
     optionList.add(new Option("refseq_protein", "refseq_protein"));
     // Use input sequence library option list if present
-    if (sequenceLibraryOptionList != null)
-    {
-      log
-        .debug("Input sequence library option list size = " + sequenceLibraryOptionList
-          .size() + " optionList.size() = " + optionList.size());
-    }
-    else
-    {
-      log
-        .debug("Input sequence library option list = null optionList.size() = " + optionList
-          .size());
-    }
     if (sequenceLibraryOptionList != null && sequenceLibraryOptionList
       .size() >= optionList.size())
     {
       optionList = sequenceLibraryOptionList;
-      log.debug("Input sequence library option list used");
-    }
-    else
-    {
-      log.debug("Default sequence library option list used");
     }
     selected = omssaParameterSet.getDb();
-    log.debug("sequence library selected = \"" + selected + "\"");
     Select<VString> sequenceLibrarySelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -4442 +4350 @@
     {
       optionList = speciesOptionList;
-      log.debug("Input species option list used");
     }
     selected = omssaParameterSet.getSpecies();
@@ -4478 +4385 @@
     {
       optionList = fixedModsOptionList;
-      log.debug("Input fixed mods option list used");
     }
     selected = omssaParameterSet.getFixed();
@@ -4504 +4410 @@
     {
       optionList = variableModsOptionList;
-      log.debug("Input variable mods option list used");
     }
     selected = omssaParameterSet.getVariable();
     selectedList = listStringToStringList(selected, delimRegex);
-    log.debug("variable mods selectedList = " + selectedList);
     Select<VString> variableMods = newStringMultipleSelectBox(
       validStringParam, optionList, selectedList);
@@ -4535 +4439 @@
     }
     selected = omssaParameterSet.getPrecursorSearchType();
-    log.debug("precursor mass search type selected = \"" + selected + "\"");
     Select<VString> precursorMassSearchTypeSelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -4548 +4451 @@
     }
     selected = omssaParameterSet.getProductSearchType();
-    log.debug("product mass search type selected = \"" + selected + "\"");
-    // selectedList = listStringToStringList(selected, delimRegex);
-    // log.debug("product mass search type selectedList = " + selectedList);
     Select<VString> productMassSearchTypeSelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -5618 +5518 @@
     {
       optionList = listPathDefaultParametersOptionList;
-      log.debug("Input list path default parameters option list used");
     }
     selected = xTandemParameterSet.getListPathDefaultParameters();
@@ -5779 +5678 @@
     {
       optionList = residueModificationMassOptionList;
-      log.debug("Input residue modification mass option list used");
     }
     selected = xTandemParameterSet.getResidueModificationMass();
@@ -5801 +5699 @@
     else
     {
-      log.debug("residue modification mass, no inserted value");
+
       modificationMass.setValue("");
     }
@@ -5876 +5774 @@
     else
     {
-      log.debug("residue potential modification mass, no inserted value");
       potentialModificationMass.setValue("");
     }
-    log
-      .debug("residue potential modification mass, potentialModificationMass.getValue() = \"" + potentialModificationMass
-        .getValue() + "\"");
     residueFS.add(potentialModificationMass);
     // Residue, potential modification motif
@@ -5932 +5826 @@
     {
       optionList = speciesOptionList;
-      log.debug("Input species option list used");
-    }
-    else
-    {
-      log.debug("Default species option list used");
     }
     selected = xTandemParameterSet.getProteinTaxon();
-    log.debug("taxon selected = \"" + selected + "\"");
     // Select<VString> taxon = newStringSelectBox2(validStringParam,
     // optionList, selected);
     selectedList = listStringToStringList(selected, ",\\ ");
-    log.debug("taxon selectedList = " + selectedList);
     Select<VString> taxon = newStringMultipleSelectBox(validStringParam,
       optionList, selectedList);
@@ -5986 +5873 @@
     {
       optionList = proSpeciesOptionList;
-      log.debug("Input Prokaryotes species option list used");
-    }
-    else
-    {
-      log.debug("Default Prokaryotes species option list used");
     }
     // Same selection list as for Eukaryotes taxon is used for Prokaryotes
-    log.debug("taxon selectedList = " + selectedList);
     Select<VString> taxon1 = newStringMultipleSelectBox(validStringParam,
       optionList, selectedList);
@@ -6020 +5901 @@
     {
       optionList = proteinCleavageSiteOptionList;
-      log.debug("Input protein cleavage site option list used");
-    }
-    else
-    {
-      log.debug("Default protein cleavage site option list used");
     }
     selected = xTandemParameterSet.getProteinCleavageSite();
-    log.debug("protein cleavage site selected = \"" + selected + "\"");
-    // selectedList = listStringToStringList(selected, ",\\ ");
-    // log.debug(""protein cleavage site selectedList = " + selectedList);
     Select<VString> proteinCleavageSiteSelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -6041 +5914 @@
     if (!itemInOptionList(optionList, selected))
     {
-      log
-        .debug("protein cleavage site, inserted value = \"" + xTandemParameterSet
-          .getProteinCleavageSite() + "\"");
       cleavageSite.setValue(xTandemParameterSet.getProteinCleavageSite());
     }
     else
     {
-      log.debug("protein cleavage site, no inserted value");
       cleavageSite.setValue("");
     }
-    log
-      .debug("protein cleavage site, cleavageSite.getValue() = \"" + cleavageSite
-        .getValue() + "\"");
     proteinFS.add(cleavageSite);
     // Protein, modified residue mass file
@@ -6219 +6085 @@
     else
     {
-      log.debug("refine potential modification mass, no inserted value");
       refinePotentialModificationMass.setValue("");
     }
-    log
-      .debug("refine potential modification mass, refinePotentialModificationMass.getValue() = \"" + refinePotentialModificationMass
-        .getValue() + "\"");
     refineFS.add(refinePotentialModificationMass);
     /** **************************************** */
@@ -6528 +6390 @@
     {
       optionList = sourceDatabaseOptionList;
-      log.debug("Input source database option list used");
-    }
-    else
-    {
-      log.debug("Default source database option list used");
     }
     selected = pikeSourceDatabase;
-    log.debug("source database selected = \"" + selected + "\"");
     Select<VString> sourceDatabaseSelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -6561 +6417 @@
     {
       optionList = fieldSelectOptionList;
-      log.debug("Input field select option list used");
-    }
-    else
-    {
-      log.debug("Default field select option list used");
     }
     selectedList = pikeFieldSelectList;
-    log.debug("field select selectedList = " + selectedList);
     Select<VString> fieldSelect = newStringMultipleSelectBox(
       validStringParam, optionList, selectedList);
@@ -6582 +6432 @@
     optionList.add(new Option("0", "no"));
     selected = pikeGeneOntologyCheck;
-    log.debug("gene ontology check selected = \"" + selected + "\"");
     Select<VString> geneOntologyCheckSelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -6604 +6453 @@
     {
       optionList = inputFileTypeOptionList;
-      log.debug("Input input file type option list used");
-    }
-    else
-    {
-      log.debug("Default input file type option list used");
     }
     selected = pikeInputFileType;
-    log.debug("input file type selected = \"" + selected + "\"");
     Select<VString> inputFileTypeSelectBox = newStringSelectBox2(
       validStringParam, optionList, selected);
@@ -6632 +6475 @@
     {
       optionList = outputFileTypeOptionList;
-      log.debug("Input output file type option list used");
-    }
-    else
-    {
-      log.debug("Default output file type option list used");
     }
     selectedList = pikeOutputFileTypeList;
-    log.debug("output file type selectedList = " + selectedList);
     Select<VString> outputFileTypeSelect = newStringMultipleSelectBox(
       validStringParam, optionList, selectedList);
@@ -7178 +7015 @@
      */
     Form form = null;
-    log
-      .debug("FormFactory::getForm(): Start =====================================");
-    if (template == null)
-    {
-      log.debug("FormFactory::getForm(): template  == null");
-    }
     if (template instanceof FormTemplateImpl)
     {
-      log
-        .debug("FormFactory::getForm(): template instance of FormTemplateImpl");
       FormTemplateImpl formTemplate = (FormTemplateImpl) template;
       form = getFormImpl(formTemplate);
     }
-    else
-    {
-      log
-        .debug("FormFactory::getForm(): template not instance of FormTemplateImpl");
-    }
-    /*
-     * Return generated form.
-     */
     return form;
   }
@@ -7214 +7035 @@
      * Analyze object class
      */
-    if (formTemplate == null)
-    {
-      log.debug("FormFactory::getFormImpl(): formTemplate  == null");
-      return null;
-    }
-    log
-      .debug("FormFactory::getFormImpl(): Start =====================================");
-    log
-      .debug("FormFactory::getFormImpl(): formTemplate.getItemObject() = \"" + formTemplate
-        .getItemObject() + "\"");
-    log
-      .debug("FormFactory::getFormImpl(): formTemplate.getItemClass() = \"" + formTemplate
-        .getItemClass() + "\"");
-    log
-      .debug("FormFactory::getFormImpl(): formTemplate.isReadOnlyForm = " + formTemplate
-        .isReadOnlyForm());
-    if (formTemplate.getExcludedDeclMethods() == null)
-    {
-      log
-        .debug("FormFactory::getFormImpl(): formTemplate.getExcludedDeclMethods() == null");
-    }
-    else
-    {
-      log
-        .debug("FormFactory::getFormImpl(): formTemplate.getExcludedDeclMethods().size() = " + formTemplate
-          .getExcludedDeclMethods().size());
-      for (int i = 0; i < formTemplate.getExcludedDeclMethods().size(); i++)
-      {
-        log
-          .debug("FormFactory::getFormImpl(): formTemplate.getExcludedDeclMethods().get(" + i + ") = \"" + formTemplate
-            .getExcludedDeclMethods().get(i) + "\"");
-      }
-    }
+
     /*
      * Get class from formTemplate itemObject or itemClass.
@@ -7268 +7057 @@
       addExcludedDeclMethods(formTemplate.getExcludedDeclMethods());
     }
-    log
-      .debug("FormFactory::getFormImpl(): (After checking for itemObject) itemClass = \"" + itemClass + "\"");
     String clsName = new String("");
     if (itemClass != null)
@@ -7275 +7062 @@
       clsName = itemClass.getSimpleName();
     }
-    log.debug("FormFactory::getFormImpl(): clsName = \"" + clsName + "\"");
+
     /***********************************************************************
      * Main fieldset
@@ -7281 +7068 @@
     Fieldset mainFS = new Fieldset();
     String mainFsName = new String("Properties");
-    // if (clsName != null && !clsName.equals(""))
-    // {
-    // mainFsName = clsName;
-    // }
     mainFS.setTitle(mainFsName);
     /*
@@ -7309 +7092 @@
       catch (InvocationTargetException e)
       {
-        log
-          .warn("FormFactory::getFormImpl(): InvocationTargetException when invoking method \"" + getIdMethodName + "\":" + e);
         itemId = 0;
       }
       catch (IllegalAccessException e)
       {
-        log
-          .warn("FormFactory::getFormImpl(): IllegalAccessException when invoking method \"" + getIdMethodName + "\":" + e);
         itemId = 0;
       }
       catch (java.lang.NumberFormatException e)
       {
-        log
-          .warn("FormFactory::getFormImpl(): NumberFormatException when invoking method \"" + getIdMethodName + "\":" + e);
         itemId = 0;
       }
@@ -7336 +7113 @@
       idF.setValue(itemId);
       idF.setDisabled(true);
-      log
-        .debug("FormFactory::getFormImpl(): Hidden TextField idF set to " + itemId);
-    }
-    else
-    {
-      log
-        .debug("FormFactory::getFormImpl(): Hidden TextField idF NOT set, itemId = " + itemId);
     }
     /*
@@ -7358 +7128 @@
     cnF.setValue(classNameFull);
     cnF.setDisabled(true);
-    log
-      .debug("FormFactory::getFormImpl(): Hidden TextField cnF set to \"" + classNameFull + "\"");
     /*
      * Add readOnlyForm field rofF (hidden).
@@ -7368 +7136 @@
     rofF.setValue(formTemplate.isReadOnlyForm());
     rofF.setDisabled(true);
-    log
-      .debug("FormFactory::getFormImpl(): Hidden TextField rofF (readOnlyForm field) set to " + formTemplate
-        .isReadOnlyForm());
     /*
      * Keep track on whether public setter methods exist, in order to know
@@ -7461 +7226 @@
           }
         }
-        log
-          .debug("FormFactory::getFormImpl(): methodName = \"" + methodName + "\"  returnTypeOfGetterMethod = \"" + returnTypeOfGetterMethod + "\" returnTypeStr = \"" + returnTypeStr + "\" returnTypeOK = " + returnTypeOK);
         if (returnTypeOK)
         {
@@ -7566 +7329 @@
       }
     }
-    for (int i = 0; i < declaredMethodArr.length; i++)
-    {
-      Method method = declaredMethodArr[i];
-      String modStr = methodModifierString(method);
-      String methodName = method.getName();
-      String methodReturnType = method.getReturnType().getName();
-      if (getExcludedDeclMethods().contains(methodName))
-      {
-        log
-          .debug("FormFactory::getFormImpl(): *Excluded* " + modStr + " " + methodReturnType + " declaredMethodArr[" + i + "].getName() = \"" + methodName + "\"");
-      }
-    }
+
     /*
      * Check if object supports method getAnnotationSet().
@@ -7587 +7339 @@
       methodGeneralArr = itemClass.getMethods();
     }
-    log
-      .debug("FormFactory::getFormImpl(): methodGeneralArr.length = " + methodGeneralArr.length);
     for (int i = 0; i < methodGeneralArr.length; i++)
     {
@@ -7658 +7408 @@
         .substring(1, clsName.length()) + "Form";
     }
-    log
-      .debug("FormFactory::getFormImpl(): formName = \"" + formName + "\"");
     Form form = new Form(formName);
     form.setTitle(clsName);
@@ -7670 +7418 @@
       form.addFieldset(annotationFS);
     }
-    log
-      .debug("FormFactory::getFormImpl(): hasSetterMethods = " + hasSetterMethods);
     /*
      * Return generated form.
@@ -7699 +7445 @@
     }
     String clsName = cls.getSimpleName();
-    log
-      .debug("FormFactory::getDbControlForObject(): clsName = \"" + clsName + "\"");
     /*
      * Check if object supports method getDbControl().
@@ -7706 +7450 @@
     DbControl dc = null;
     Method[] methodGeneralArr = cls.getMethods();
-    log
-      .debug("FormFactory::getDbControlForObject(): methodGeneralArr.length = " + methodGeneralArr.length);
     for (int i = 0; i < methodGeneralArr.length; i++)
     {
@@ -7752 +7494 @@
       Class<? extends Object> cls)
   {
-    log
-      .debug("FormFactory::fetchPublicMethodForObject(): publMethodName = \"" + publMethodName + "\"");
     if (cls == null)
     {
@@ -7759 +7499 @@
     }
     String clsName = cls.getSimpleName();
-    log
-      .debug("FormFactory::fetchPublicMethodForObject(): clsName = \"" + clsName + "\"");
     /*
      * Check if object supports public method with desired name.
@@ -7782 +7520 @@
       }
     }
-    /*
-     * Return method.
-     */
-    if (publMethod == null)
-    {
-      log
-        .debug("FormFactory::fetchPublicMethodForObject(): publMethod == null");
-    }
-    else
-    {
-      log
-        .debug("FormFactory::fetchPublicMethodForObject(): publMethod.getName() = \"" + publMethod
-          .getName() + "\"");
-    }
     return publMethod;
   }
@@ -7868 +7592 @@
       count += spectrumSearchCount;
     }
-    log.debug("FormFactory::getTrashCanForm(): dirCount = " + dirCount);
-    log.debug("FormFactory::getTrashCanForm(): fileCount = " + fileCount);
-    log.debug("FormFactory::getTrashCanForm(): jobCount = " + jobCount);
-    log
-      .debug("FormFactory::getTrashCanForm(): spectrumSearchCount = " + spectrumSearchCount);
-    log.debug("FormFactory::getTrashCanForm(): count = " + count);
     // Add info line(s) on number of items of each class to delete
     if (count == 0)
@@ -8601 +8319 @@
   private Select<VInteger> getProtocolSelectBox(Class cls, Object obj)
   {
-    log.debug("cls = " + cls + " obj = " + obj);
     Select<VInteger> protocolS = new Select<VInteger>(VPROTOCOLID);
     protocolS.setLabel("Protocol");
@@ -8635 +8352 @@
           if (mbm instanceof Extract)
           {
-            log.debug("MeasuredBioMaterial instanceof Extract");
             pTypeList.add(ProtocolType.EXTRACTION);
           }
           if (mbm instanceof LabeledExtract)
           {
-            log
-              .debug("MeasuredBioMaterial instanceof LabeledExtract");
             pTypeList.add(ProtocolType.LABELING);
-          }
-          if (mbm instanceof MeasuredArea)
-          {
-            log
-              .debug("MeasuredBioMaterial instanceof MeasuredArea");
-            // pTypeList.add(ProtocolType.EXTRACTION);
           }
           if (mbm instanceof Sample)
           {
-            log.debug("MeasuredBioMaterial instanceof Sample");
             pTypeList.add(ProtocolType.SAMPLING);
           }
-          log.debug("MeasuredBioMaterial is pooled = " + mbm
-            .isPooled());
           if (mbm.isPooled())
           {
@@ -8664 +8369 @@
       }
     }
-    log.debug("pTypeList = " + pTypeList);
     // Get optional input protocol
     Protocol inProtocol = null;
@@ -8671 +8375 @@
       BioMaterialEvent<?> bme = (BioMaterialEvent<?>) obj;
       inProtocol = bme.getProtocol();
-    }
-    if (inProtocol != null)
-    {
-      log
-        .debug("inProtocol = " + inProtocol + " inProtocol.isRemoved() = " + inProtocol
-          .isRemoved());
-    }
-    else
-    {
-      log.debug("inProtocol = " + inProtocol);
     }
     // Get protocols
@@ -8824 +8518 @@
   {
     List<String> stringList = null;
-    log
-      .debug("listString = \"" + listString + "\" delimiterRegex = \"" + delimiterRegex + "\"");
     if (listString != null)
     {
@@ -8831 +8523 @@
       for (String part : listString.split(delimiterRegex, -1))
       {
-        log.debug("part = \"" + part + "\"");
         // Add list part if not already in list
         if (part != null && !stringList.contains(part))
@@ -8839 +8530 @@
       }
     }
-    log.debug("stringList = " + stringList);
     return stringList;
   }