Changeset 3906


Ignore:
Timestamp:
Oct 21, 2010, 10:58:34 AM (13 years ago)
Author:
olle
Message:

Refs #700. Changes added to class ViewActiveXTandemParameterSetStorage and dictionary file in
changeset ​[3904]
in connection with first version of support for simple
X!Tandem search form reverted, in preparation for new version of the
routine using a single form:

  1. Class/file action/xTandemInputViewActiveXTandemParameterSetStorage.java

in client/servlet/ restored to previous version, except for removal of unused imports.

  1. English dictionary file locale/en/dictionary in client/servlet/ updated by removal of entries for first version of support for

simple X!Tandem search form.

Location:
trunk/client/servlet/src
Files:
2 edited

Legend:

Unmodified
Added
Removed

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

    r3904 r3906  
    5151Address=Address
    5252Administrator=Administrator
    53 AdvancedSearchForm=Advanced Search Form
    5453All=All
    5554AllowedFDR=Allowed FDR
    … …  
    771770Show=Show
    772771SignalToNoiseRatio=S/N
    773 SimpleSearchForm=Simple Search Form
    774772SizeInBytes=Size (bytes)
    775773Size=Size

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

    r3904 r3906  
    4444import se.lu.thep.waf.ActionException;
    4545import se.lu.thep.waf.constraints.InvalidParameterValue;
    46 import se.lu.thep.waf.constraints.VBoolean;
    4746import se.lu.thep.waf.constraints.VInteger;
    48 import se.lu.thep.waf.constraints.VString;
    4947
    5048/**
    … …  
    5654  public static final VInteger VXTANDEMPARAMETERSETSTORAGEID = new VInteger(
    5755    "active.xtandemparametersetstorage.id", 1, false);
    58   public static final VBoolean VXTANDEMPARAMETERSETSIMPLEFORMFLAG = new VBoolean(
    59     "active.xtandemparametersetstoragesimpleformflag", false);
    6056
    6157
    … …  
    8884    List<Integer> spectrumFileIds = getValidIntegerList(SearchXTandem.VSPECTRUMFILEID);
    8985    log.debug("spectrumFileIds = " + spectrumFileIds);
    90     // Get the useSimpleForm flag
    91     Boolean useSimpleForm = getValidBoolean(VXTANDEMPARAMETERSETSIMPLEFORMFLAG);
    92     log.debug("useSimpleForm from VXTANDEMPARAMETERSETSIMPLEFORMFLAG = " + useSimpleForm);
    93     boolean firstEntry = false;
    94     if (useSimpleForm == null)
    95     {
    96       // Default form type is simple form
    97       useSimpleForm = true;
    98       firstEntry = true;
    99     }
    100     log.debug("useSimpleForm = " + useSimpleForm);
    101     log.debug("firstEntry = " + firstEntry);
    10286    //
    10387    DbControl dc = newDbControl();
    … …  
    10993    xTandemParameterFileUtil.setXMLInputStream(iStream);
    11094    XTandemParameterSet xTandemParameterSet = xTandemParameterFileUtil.fetchXTandemParameterSet();
    111     // Get X!Tandem parameter set display form
    112     Form xTandemParameterSetDisplayForm;
    113     if (useSimpleForm)
    114     {
    115       log.debug("### Simple X!Tandem Parameter Set Form");
    116       // Use simple X!Tandem parameter set form
    117       if (firstEntry)
    118       {
    119         // Fill in form fields with data from stored X!Tandem parameter set
    120         Form xTandemParameterSetFormSimple = new XTandemParameterSetFormSimple(xTandemParameterSet);
    121         xTandemParameterSetDisplayForm = xTandemParameterSetFormSimple;
    122       }
    123       else
    124       {
    125         // Fill in form fields with data from previously displayed simple/advanced form
    126         Form xTandemParameterSetFormSimple = new XTandemParameterSetFormSimple();
    127         populateForm(xTandemParameterSetFormSimple);
    128         xTandemParameterSetFormSimple = updateSimpleFormMultipleChoiceFields((XTandemParameterSetFormSimple) xTandemParameterSetFormSimple);
    129         xTandemParameterSetDisplayForm = xTandemParameterSetFormSimple;
    130       }
    131     }
    132     else
    133     {
    134       log.debug("### Advanced X!Tandem Parameter Set Form");
    135       // Use advanced X!Tandem parameter set form
    136       if (firstEntry)
    137       {
    138         // Fill in form fields with data from stored X!Tandem parameter set       
    139         Form xTandemParameterSetForm = new XTandemParameterSetForm(xTandemParameterSet);
    140         xTandemParameterSetDisplayForm = xTandemParameterSetForm;
    141       }
    142       else
    143       {
    144         // Fill in form fields with data from previously displayed simple/advanced form
    145         Form xTandemParameterSetForm = new XTandemParameterSetForm();
    146         populateForm(xTandemParameterSetForm);
    147         xTandemParameterSetForm = updateAdvancedFormMultipleChoiceFields((XTandemParameterSetForm) xTandemParameterSetForm);
    148         xTandemParameterSetDisplayForm = xTandemParameterSetForm;
    149       }
    150     }
     95    Form xTandemParameterSetForm = new XTandemParameterSetForm(xTandemParameterSet);
    15196    /***********************************************************************
    15297     * Annotations table
    … …  
    193138      for (Integer spectrumFileId : spectrumFileIds)
    194139      {
    195         getFormFactory().addHiddenField(xTandemParameterSetDisplayForm, SearchXTandem.VSPECTRUMFILEID, spectrumFileId);
     140        getFormFactory().addHiddenField(xTandemParameterSetForm, SearchXTandem.VSPECTRUMFILEID, spectrumFileId);
    196141      }
    197142      searchXTandemViaWebInterface.addParameter(SearchXTandem.VXTANDEMUSEWEBINTERFACEFLAG, true);
    … …  
    223168      */
    224169    }
    225     // Add button to toggle between simple/advanced form
    226     String toggleFormTypeButtonLabel;
    227     if (useSimpleForm)
    228     {
    229       toggleFormTypeButtonLabel = new String("AdvancedSearchForm");
    230     }
    231     else
    232     {
    233       toggleFormTypeButtonLabel = new String("SimpleSearchForm");
    234     }
    235     ActionLink toggleFormTypeButton = getActionLink(ViewActiveXTandemParameterSetStorage.class, toggleFormTypeButtonLabel);
    236     toggleFormTypeButton.addParameter(VXTANDEMPARAMETERSETSIMPLEFORMFLAG, !useSimpleForm);
    237     toggleFormTypeButton.addParameter(VXTANDEMPARAMETERSETSTORAGEID, xtpssId);
    238     toolbar.add(toggleFormTypeButton);
    239     // Add tool bar
    240     xTandemParameterSetDisplayForm.setToolbar(toolbar);
     170    xTandemParameterSetForm.setToolbar(toolbar);
    241171    /***********************************************************************
    242172     * Layout
    … …  
    252182    ts.add(annotations);
    253183    */
    254     layout.add(xTandemParameterSetDisplayForm);
     184    layout.add(xTandemParameterSetForm);
    255185    setLayout(layout);
    256186  }
    257 
    258 
    259   /**
    260    * Update advanced form multiple choice fields.
    261    *
    262    * @param form XTandemParameterSetForm An advanced X!Tandem parameter set form.
    263    * @return XTandemParameterSetForm The updated form.
    264    */
    265   private XTandemParameterSetForm updateAdvancedFormMultipleChoiceFields(XTandemParameterSetForm form)
    266   {
    267     List<String> stringList;
    268     // Residue potential modification mass
    269     stringList = fetchValidStringList("residue potential modification mass",
    270       XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT);
    271     if (stringList != null)
    272     {
    273       form.residuePotentialModificationMassSB.selectOptions(stringList);
    274     }
    275     // Protein taxon Eukaryotes
    276     stringList = fetchValidStringList("protein taxon Eukaryotes",
    277       XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON);
    278     if (stringList != null)
    279     {
    280       form.taxonSB.selectOptions(stringList);
    281     }
    282     // Protein taxon Prokaryotes
    283     stringList = fetchValidStringList("protein taxon Prokaryotes",
    284       XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON1);
    285     if (stringList != null)
    286     {
    287       form.taxon1SB.selectOptions(stringList);
    288     }
    289     // Refine potential modification mass
    290     List<Option> startList = form.refinePotentialModificationMassSB.getOptions();
    291     if (startList != null)
    292     {
    293       log.debug("Start - refine potential modification mass select list size: " + startList.size());     
    294       for (Option opt: startList)
    295       {
    296         if (opt.isSelected())
    297         {
    298           log.debug("Start - refine potential modification mass selected: \"" + opt.getValue() + "\" content: \"" + opt.getValue() + "\"");
    299         }
    300       }
    301     }
    302     stringList = fetchValidStringList("refine potential modification mass",
    303       XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
    304     log.debug("refine potential modification mass select list = " + stringList);
    305     if (stringList != null)
    306     {
    307       log.debug("refine potential modification mass select field list size = " + stringList.size());
    308       form.refinePotentialModificationMassSB.selectOptions(stringList);
    309     }
    310     return form;
    311   }
    312 
    313 
    314   /**
    315    * Update simple form multiple choice fields.
    316    *
    317    * @param form XTandemParameterSetFormSimple A simple X!Tandem parameter set form.
    318    * @return XTandemParameterSetFormSimple The updated form.
    319    */
    320   private XTandemParameterSetFormSimple updateSimpleFormMultipleChoiceFields(XTandemParameterSetFormSimple form)
    321   {
    322     List<String> stringList;
    323     // Residue potential modification mass
    324     stringList = fetchValidStringList("residue potential modification mass",
    325       XTandemParameterSetForm.VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS_SELECT);
    326     if (stringList != null)
    327     {
    328       form.residuePotentialModificationMassSB.selectOptions(stringList);
    329     }
    330     // Protein taxon Eukaryotes
    331     stringList = fetchValidStringList("protein taxon Eukaryotes",
    332       XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON);
    333     if (stringList != null)
    334     {
    335       form.taxonSB.selectOptions(stringList);
    336     }
    337     // Protein taxon Prokaryotes
    338     stringList = fetchValidStringList("protein taxon Prokaryotes",
    339       XTandemParameterSetForm.VXTANDEM_PROTEIN_TAXON1);
    340     if (stringList != null)
    341     {
    342       form.taxon1SB.selectOptions(stringList);
    343     }
    344     // Refine potential modification mass
    345     stringList = fetchValidStringList("refine potential modification mass",
    346       XTandemParameterSetForm.VXTANDEM_REFINE_POTENTIAL_MODIFICATION_MASS_SELECT);
    347     log.debug("refine potential modification mass select list = " + stringList);
    348     if (stringList != null)
    349     {
    350       form.refinePotentialModificationMassSB.selectOptions(stringList);
    351     }
    352     return form;
    353   }
    354 
    355 
    356   /**
    357    * Convenience method for fetching string list from request.
    358    *
    359    * @param quantityName String Name of the list quantity.
    360    * @param param VString Valid parameter coupled to the list.
    361    * @return List<String> The string list obtained from the request.
    362    */
    363   private List<String> fetchValidStringList(String quantityName, VString param)
    364   {
    365     // Fetch string list from request
    366     List<String> stringList = null;
    367     try
    368     {
    369       stringList = getValidStringList(param);
    370       log.debug(quantityName + " = " + stringList);
    371     }
    372     catch (InvalidParameterValue e)
    373     {
    374       log.debug("InvalidParameterValue when trying to obtain " + quantityName);
    375     }
    376     return stringList;
    377   }
    378187}
Note: See TracChangeset for help on using the changeset viewer.