Changeset 3767

Timestamp:

Aug 16, 2010, 3:00:39 PM (13 years ago)

Author:

Gregory Vincic

Message:

Refs #685. Refactoring action class ViewActiveMascotParameterSetStorage?

File:

• trunk/client/servlet/src/org/proteios/action/mascot/ViewActiveMascotParameterSetStorage.java (modified) (9 diffs)

trunk/client/servlet/src/org/proteios/action/mascot/ViewActiveMascotParameterSetStorage.java

@@ -63 +63 @@
       throws ActionException, InvalidParameterValue
   {
-    /***********************************************************************
-     * Properties
-     */
     // Get the MascotParameterSetStorage item to use for the search
-    Integer mascotpssId = getValidInteger(VMASCOTPARAMETERSETSTORAGEID);
+    Integer mascotpssId;
+  Boolean useWebInterfaceFlag;
+  String mascotSearchUserName, mascotSearchUserEmail;
+  DbControl dc;
+  ItemFactory factory;
+  MascotParameterSetStorage mascotpss;
+  MascotParameterFileUtil fileUtil;
+  InputStream iStream;
+  MascotParameterSet mascotParameterSet;
+  MascotParameterSetOptionsUtil util;
+  Form mascotParameterSetForm;
+  Toolbar toolbar;
+  ActionLink save,saveAs,searchMascot,saveAsAndSearchMascot;
+  RowLayout layout;
+  Title title;
+  List<Integer> spectrumFileIds, mascotpssIds;
+  List<String> enzymeStringList;
+  List<Option> enzymeOptionList;
+  List<String> missedCleavagesStringList;
+  List<Option> missedCleavagesOptionList;
+  List<String> sequenceLibraryStringList;
+  List<Option> sequenceLibraryOptionList;
+  List<String> speciesStringList;
+  List<Option> speciesOptionList;
+  List<String> fixedModsStringList;
+  List<Option> fixedModsOptionList;
+  List<String> variableModsStringList;
+  List<Option> variableModsOptionList;
+  List<String> quantitationStringList;
+  List<Option> quantitationOptionList;
+  List<String> peptideTolUnitStringList;
+  List<Option> peptideTolUnitOptionList;
+  List<String> peptideIsotopeErrorStringList;
+  List<Option> peptideIsotopeErrorOptionList;
+  List<String> msMsTolUnitStringList;
+  List<Option> msMsTolUnitOptionList;
+  List<String> peptideChargeStringList;
+  List<Option> peptideChargeOptionList;
+  List<String> dataFormatStringList;
+  List<Option> dataFormatOptionList;
+  List<String> instrumentStringList;
+  List<Option> instrumentOptionList;
+  List<String> reportTopStringList;
+  List<Option> reportTopOptionList;
+  // Define
+
+  mascotpssId = getValidInteger(VMASCOTPARAMETERSETSTORAGEID);
+    useWebInterfaceFlag = getValidBoolean(SearchMascot.VMASCOTUSEWEBINTERFACEFLAG);
+
+    if (useWebInterfaceFlag == null)
+    {
+      useWebInterfaceFlag = true;
+    }
+    // Optional Mascot search user data
+    mascotSearchUserName = getValidString(SearchMascot.VMASCOT_SEARCH_USER_NAME);
+    mascotSearchUserEmail = getValidString(SearchMascot.VMASCOT_SEARCH_USER_EMAIL);
+
     log.debug("mascotParameterSetStorageId from VMASCOTPARAMETERSETSTORAGEID = " + mascotpssId);
-    // Get the MascotParameterSetStorage item to use for the search
-    Boolean useWebInterfaceFlag = getValidBoolean(SearchMascot.VMASCOTUSEWEBINTERFACEFLAG);
     log.debug("useWebInterfaceFlag from SearchMascot.VMASCOTUSEWEBINTERFACEFLAG = " + useWebInterfaceFlag);
-    if (useWebInterfaceFlag == null)
-    {
-      useWebInterfaceFlag = true;
-    }
     log.debug("useWebInterfaceFlag = " + useWebInterfaceFlag);
-    // SearchMascot.VMASCOTUSEWEBINTERFACEFLAG
-    // Get optional Mascot search user data
-    String mascotSearchUserName = getValidString(SearchMascot.VMASCOT_SEARCH_USER_NAME);
-    String mascotSearchUserEmail = getValidString(SearchMascot.VMASCOT_SEARCH_USER_EMAIL);
     log.debug("mascotSearchUserName = \"" + mascotSearchUserName + "\"");
     log.debug("mascotSearchUserEmail = \"" + mascotSearchUserEmail + "\"");
@@ -86 +129 @@
     if (mascotpssId == null || mascotpssId == 0)
     {
-      List<Integer> mascotpssIds = getValidIntegerList(FormFactory.VID);
+      mascotpssIds = getValidIntegerList(FormFactory.VID);
       log.debug("mascotpssIds from FormFactory.VID = " + mascotpssIds);
       // Make sure at least one file has been selected
@@ -99 +142 @@
     log.debug("mascotpssId = " + mascotpssId);
     // Get the spectrum file items to use for the search
-    List<Integer> spectrumFileIds = getValidIntegerList(SearchMascot.VSPECTRUMFILEID);
+    spectrumFileIds = getValidIntegerList(SearchMascot.VSPECTRUMFILEID);
     log.debug("spectrumFileIds = " + spectrumFileIds);
-    //
-    DbControl dc = newDbControl();
-    ItemFactory factory = getItemFactory(dc);
-    MascotParameterSetStorage mascotpss = factory.getById(MascotParameterSetStorage.class, mascotpssId);
+    dc = newDbControl();
+    factory = getItemFactory(dc);
+    mascotpss = factory.getById(MascotParameterSetStorage.class, mascotpssId);
     // Get Mascot parameter data from xml file
-    MascotParameterFileUtil mascotParameterFileUtil = new MascotParameterFileUtil();
-    InputStream iStream = mascotpss.getParameterFile().getDownloadStream(0);
-    mascotParameterFileUtil.setXMLInputStream(iStream);
-    MascotParameterSet mascotParameterSet = mascotParameterFileUtil.fetchMascotParameterSet();
-    // Get Mascot parameter set option alternatives
+    fileUtil = new MascotParameterFileUtil();
+    iStream = mascotpss.getParameterFile().getDownloadStream(0);
+    fileUtil.setXMLInputStream(iStream);
+    mascotParameterSet = fileUtil.fetchMascotParameterSet();
     // Get MascotParameterSetOptionsUtil instance
-    MascotParameterSetOptionsUtil mascotParameterSetOptionUtil = new MascotParameterSetOptionsUtil(mascotParameterSet.getSearchType());
-    mascotParameterSetOptionUtil.setWebInterfaceUsed(useWebInterfaceFlag);
+    util = new MascotParameterSetOptionsUtil(mascotParameterSet.getSearchType());
+    util.setWebInterfaceUsed(useWebInterfaceFlag);
     // Get enzyme option data
-    List<String> enzymeStringList = mascotParameterSetOptionUtil.fetchEnzymeStringList();
-    List<Option> enzymeOptionList = stringListToOptionList(enzymeStringList);
+    enzymeStringList = util.fetchEnzymeStringList();
+    enzymeOptionList = stringListToOptionList(enzymeStringList);
     // Get missed cleavages option data
-    List<String> missedCleavagesStringList = mascotParameterSetOptionUtil.fetchMissedCleavagesStringList();
-    List<Option> missedCleavagesOptionList = stringListToOptionList(missedCleavagesStringList);
+    missedCleavagesStringList = util.fetchMissedCleavagesStringList();
+    missedCleavagesOptionList = stringListToOptionList(missedCleavagesStringList);
     // Get sequence library option data
-    List<String> sequenceLibraryStringList = mascotParameterSetOptionUtil.fetchSequenceLibraryStringList();
-    List<Option> sequenceLibraryOptionList = stringListToOptionList(sequenceLibraryStringList);
+    sequenceLibraryStringList = util.fetchSequenceLibraryStringList();
+    sequenceLibraryOptionList = stringListToOptionList(sequenceLibraryStringList);
     // Get species option data
-    List<String> speciesStringList = mascotParameterSetOptionUtil.fetchSpeciesStringList();
-    List<Option> speciesOptionList = stringListToOptionList(speciesStringList);
+    speciesStringList = util.fetchSpeciesStringList();
+    speciesOptionList = stringListToOptionList(speciesStringList);
     // Get fixed modifications option data
-    List<String> fixedModsStringList = mascotParameterSetOptionUtil.fetchModificationStringList();
-    List<Option> fixedModsOptionList = stringListToOptionList(fixedModsStringList);
+    fixedModsStringList = util.fetchModificationStringList();
+    fixedModsOptionList = stringListToOptionList(fixedModsStringList);
     // Get variable modifications option data
-    List<String> variableModsStringList = mascotParameterSetOptionUtil.fetchModificationStringList();
-    List<Option> variableModsOptionList = stringListToOptionList(variableModsStringList);
+    variableModsStringList = util.fetchModificationStringList();
+    variableModsOptionList = stringListToOptionList(variableModsStringList);
     // Get quantitation option data
-    List<String> quantitationStringList = mascotParameterSetOptionUtil.fetchQuantitationStringList();
-    List<Option> quantitationOptionList = stringListToOptionList(quantitationStringList);
+    quantitationStringList = util.fetchQuantitationStringList();
+    quantitationOptionList = stringListToOptionList(quantitationStringList);
     // Get peptide tolerance unit option data
-    List<String> peptideTolUnitStringList = mascotParameterSetOptionUtil.fetchPeptideTolUnitStringList();
-    List<Option> peptideTolUnitOptionList = stringListToOptionList(peptideTolUnitStringList);
+    peptideTolUnitStringList = util.fetchPeptideTolUnitStringList();
+    peptideTolUnitOptionList = stringListToOptionList(peptideTolUnitStringList);
     // Get peptide isotope error option data
-    List<String> peptideIsotopeErrorStringList = mascotParameterSetOptionUtil.fetchPeptideIsotopeErrorStringList();
-    List<Option> peptideIsotopeErrorOptionList = stringListToOptionList(peptideIsotopeErrorStringList);
+    peptideIsotopeErrorStringList = util.fetchPeptideIsotopeErrorStringList();
+    peptideIsotopeErrorOptionList = stringListToOptionList(peptideIsotopeErrorStringList);
     // Get quantitation option data
-    List<String> msMsTolUnitStringList = mascotParameterSetOptionUtil.fetchMsMsTolUnitStringList();
-    List<Option> msMsTolUnitOptionList = stringListToOptionList(msMsTolUnitStringList);
+    msMsTolUnitStringList = util.fetchMsMsTolUnitStringList();
+    msMsTolUnitOptionList = stringListToOptionList(msMsTolUnitStringList);
     // Get peptide charge option data
-    List<String> peptideChargeStringList = mascotParameterSetOptionUtil.fetchPeptideChargeStringList();
-    List<Option> peptideChargeOptionList = stringListToOptionList(peptideChargeStringList);
+    peptideChargeStringList = util.fetchPeptideChargeStringList();
+    peptideChargeOptionList = stringListToOptionList(peptideChargeStringList);
     // Get data format option data
-    List<String> dataFormatStringList = mascotParameterSetOptionUtil.fetchDataFormatStringList();
-    List<Option> dataFormatOptionList = stringListToOptionList(dataFormatStringList);
+    dataFormatStringList = util.fetchDataFormatStringList();
+    dataFormatOptionList = stringListToOptionList(dataFormatStringList);
     // Get instrument option data
-    List<String> instrumentStringList = mascotParameterSetOptionUtil.fetchInstrumentStringList();
-    List<Option> instrumentOptionList = stringListToOptionList(instrumentStringList);
+    instrumentStringList = util.fetchInstrumentStringList();
+    instrumentOptionList = stringListToOptionList(instrumentStringList);
     // Get report top option data
-    List<String> reportTopStringList = mascotParameterSetOptionUtil.fetchReportTopStringList();
-    List<Option> reportTopOptionList = stringListToOptionList(reportTopStringList);
+    reportTopStringList = util.fetchReportTopStringList();
+    reportTopOptionList = stringListToOptionList(reportTopStringList);
     // Mascot parameter set form
-    Form mascotParameterSetForm = getFormFactory().getMascotParameterSetForm(mascotParameterSet,
+    mascotParameterSetForm = getFormFactory().getMascotParameterSetForm(mascotParameterSet,
       enzymeOptionList,
       missedCleavagesOptionList,
@@ -172 +213 @@
       instrumentOptionList,
       reportTopOptionList);
-    /***********************************************************************
-     * Annotations table
-     */
-    /*
-    Annotator anna = new Annotator(getItemFactory(dc));
-    TableFactory tableFactory = getTableFactory();
-    tableFactory.reset();
-    tableFactory.setItemClass(Annotation.class);
-    ItemQuery<Annotation> annotationQuery = anna.getAnnotationSet(mascotpss)
-      .getAnnotations();
-    tableFactory.setQuery(annotationQuery);
-    tableFactory.setMaxResults(100);
-    Table annotationsTable = tableFactory.build();
-    */
-    /***********************************************************************
+
+  /***********************************************************************
      * Toolbar
      */
-    Toolbar toolbar = new Toolbar();
+    toolbar = new Toolbar();
     if (spectrumFileIds == null)
     {
       // Save Mascot parameter set button
-      ActionLink save = getActionLink(SaveMascotParameterSetStorage.class, "Save");
+      save = getActionLink(SaveMascotParameterSetStorage.class, "Save");
       save.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
       save.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
@@ -201 +229 @@
       toolbar.add(save);
       // "Save As" Mascot parameter set button
-      ActionLink saveAs = getActionLink(SaveMascotParameterSetStorage.class, "SaveAs");
+      saveAs = getActionLink(SaveMascotParameterSetStorage.class, "SaveAs");
       saveAs.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
       saveAs.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
@@ -213 +241 @@
     {
       // Save and Search Mascot
-      ActionLink searchMascot = getActionLink(SaveMascotParameterSetStorage.class, "SaveAndSearchMascot");
+      searchMascot = getActionLink(SaveMascotParameterSetStorage.class, "SaveAndSearchMascot");
       searchMascot.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
       searchMascot.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
@@ -226 +254 @@
       toolbar.add(searchMascot);
       // "Save As" and Search Mascot
-      ActionLink saveAsAndSearchMascot = getActionLink(SaveMascotParameterSetStorage.class, "SaveAsAndSearchMascot");
+      saveAsAndSearchMascot = getActionLink(SaveMascotParameterSetStorage.class, "SaveAsAndSearchMascot");
       saveAsAndSearchMascot.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
       saveAsAndSearchMascot.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
@@ -244 +272 @@
      * Layout
      */
-    RowLayout layout = getLayoutFactory().getRowLayout();
-    Title title = new Title("MascotParameterSet");
+    layout = getLayoutFactory().getRowLayout();
+    title = new Title("MascotParameterSet");
     title.setSubtitle(mascotpss.getName());
     layout.add(title);
-    //
-    /*
-    Tab annotations = new Tab("OtherSettings", "annotationsTab");
-    annotations.setGuiElement(annotationsTable);
-    ts.add(annotations);
-    */
-    layout.add(mascotParameterSetForm);
+  layout.add(mascotParameterSetForm);
     setLayout(layout);
   }
@@ -272 +294 @@
       return null;
     }
-    List<Option> optionList = new ArrayList<Option>(0);
+    List<Option> optionList = new ArrayList<Option>(stringList.size());
     for (int i = 0; i < stringList.size(); i = i + 2)
     {