Changeset 3861


Ignore:
Timestamp:
Sep 20, 2010, 8:50:06 AM (13 years ago)
Author:
Gregory Vincic
Message:

Refs #698. Removed method getSaveAsMascotParameterSetStorageFrom from FormFactory.

Location:
trunk/client/servlet/src/org/proteios
Files:
1 added
2 edited

Legend:

Unmodified
Added
Removed

  • trunk/client/servlet/src/org/proteios/action/mascot/SaveMascotParameterSetStorage.java

    r3828 r3861  
    185185        log.debug("mascotpss.getParameterFile() = \"" + mascotpss.getParameterFile() + "\"");
    186186        // MascotParameterSetStorage form
    187         form = getFormFactory().getSaveAsMascotParameterSetStorageForm(mascotpss, mascotParameterSet);
     187        form = new MascotSaveAsForm(mascotpss, mascotParameterSet);
    188188        // Toolbar
    189189        tb = new Toolbar();

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

    r3859 r3861  
    23352335  }
    23362336
    2337  // Cleaning up from here
    2338 
    2339 
    2340   /**
    2341    * Form for saving a MascotParameterSetStorage item under a new name. This
    2342    * method only uses the mascotParameterSet argument as a convenient place
    2343    * holder for default values for the MascotParameterSet form fields.
    2344    *
    2345    * @param mascotParameterSetStorage MascotParameterSetStorage object with
    2346    *        default field values for name and parameter template file.
    2347    * @param mascotParameterSet MascotParameterSet object (need not be stored
    2348    *        in database) with default field values.
    2349    * @return Form A form for setting MascotParameterSetStorage values.
    2350    */
    2351   public Form getSaveAsMascotParameterSetStorageForm(
    2352       MascotParameterSetStorage mascotParameterSetStorage,
    2353       MascotParameterSet mascotParameterSet)
    2354   {
    2355     Form form = new Form("SaveAsMascotParameterSetStorage");
    2356     form.setTitle("SaveAsMascotParameterSetStorage");
    2357     Fieldset fs = new Fieldset("SaveAsMascotParameterSetStorage");
    2358     // MascotParameterSetStorage Name
    2359     TextField<String> nameF = new NameField("Mascot parameter set storage");
    2360     fs.add(nameF);
    2361     if (mascotParameterSetStorage != null)
    2362     {
    2363       nameF.setValue(mascotParameterSetStorage.getName());
    2364     }
    2365     // MascotParameterSetStorage Description
    2366     TextArea descF = new DescriptionField();
    2367     fs.add(descF);
    2368     descF.setValue("Mascot parameter set storage");
    2369     if (mascotParameterSetStorage != null)
    2370     {
    2371       descF.setValue(mascotParameterSetStorage.getDescription());
    2372     }
    2373     // Mascot Parameters Template File
    2374     TextField<String> parameterFileF = new FileNameField();
    2375     fs.add(parameterFileF);
    2376     parameterFileF.setLabel("MascotParameterTemplateFile");
    2377     parameterFileF.setValue(getLocale().get("NotSpecifiedDefaultUsed"));
    2378     if (mascotParameterSetStorage != null)
    2379     {
    2380       if (mascotParameterSetStorage.getParameterFile() != null)
    2381       {
    2382         parameterFileF.setValue(mascotParameterSetStorage
    2383           .getParameterFile().getPath().toString());
    2384       }
    2385     }
    2386     parameterFileF.setDisabled(true);
    2387     // Mascot Parameters Template File id
    2388     TextField<Integer> parameterFileIdF = new TextField<Integer>(AddMascotParameterSetStorage.VMASCOTPARAMETERTEMPLATEFILEID);
    2389     fs.add(parameterFileIdF);
    2390     parameterFileIdF.setHidden(true);
    2391     parameterFileIdF.setLabel("MascotParameterTemplateFileId");
    2392     parameterFileIdF.setValue(0);
    2393     if (mascotParameterSetStorage != null)
    2394     {
    2395       if (mascotParameterSetStorage.getParameterFile() != null)
    2396       {
    2397         parameterFileIdF.setValue(mascotParameterSetStorage
    2398           .getParameterFile().getId());
    2399       }
    2400     }
    2401     // Hidden text field for initial mascotParameterSetStorage id
    2402     TextField<Integer> iniMascotpssIdF = new TextField<Integer>(
    2403       ViewActiveMascotParameterSetStorage.VMASCOTPARAMETERSETSTORAGEID);
    2404     iniMascotpssIdF.setHidden(true);
    2405     if (mascotParameterSetStorage != null)
    2406     {
    2407       iniMascotpssIdF.setValue(mascotParameterSetStorage.getId());
    2408     }
    2409     fs.add(iniMascotpssIdF);
    2410     // Hidden text fields for transferring values of Mascot parameter set
    2411     boolean fieldsHidden = true;
    2412     boolean fieldsDisabled = false;
    2413     fs = addMascotParameterSetToFieldset(mascotParameterSet, fs,
    2414       fieldsHidden, fieldsDisabled);
    2415     //
    2416     form.addFieldset(fs);
    2417     return form;
    2418   }
    2419 
    2420 
    2421   /**
    2422    * Convenience method for adding MascotParameterSet fields to a Fieldset.
    2423    *
    2424    * @param mascotParameterSet MascotParameterSet object (need not be stored
    2425    *        in database) with default field values.
    2426    * @param fs Fieldset The Fieldset to add the MascotParameterSet fields to.
    2427    * @param fieldsHidden boolean Flag indicating that added fields should be
    2428    *        hidden.
    2429    * @param fieldsDisabled boolean Flag indicating that added fields should be
    2430    *        disabled.
    2431    * @return Fieldset The input fieldset with added MascotParameterSet fields.
    2432    */
    2433   public Fieldset addMascotParameterSetToFieldset(
    2434       MascotParameterSet mascotParameterSet, Fieldset fs,
    2435       boolean fieldsHidden, boolean fieldsDisabled)
    2436   {
    2437     // Search type
    2438     fs.add( new TextField<String>(
    2439       SaveMascotParameterSetStorage.VMASCOT_SEARCH_TYPE,
    2440       mascotParameterSet.getSearchType(), fieldsHidden,
    2441       fieldsDisabled));
    2442     // Search title
    2443     fs.add( new TextField<String>(
    2444       SaveMascotParameterSetStorage.VMASCOT_SEARCH_TITLE,
    2445       mascotParameterSet.getSearchTitle(), fieldsHidden,
    2446       fieldsDisabled));
    2447     // Sequence library
    2448     fs.add( new TextField<String>(
    2449       SaveMascotParameterSetStorage.VMASCOT_DB, mascotParameterSet
    2450         .getDb(), fieldsHidden, fieldsDisabled));
    2451     // Species (taxon)
    2452     fs.add( new TextField<String>(
    2453       SaveMascotParameterSetStorage.VMASCOT_SPECIES, mascotParameterSet
    2454         .getSpecies(), fieldsHidden, fieldsDisabled));
    2455     // Enzyme
    2456     fs.add( new TextField<String>(
    2457       SaveMascotParameterSetStorage.VMASCOT_ENZYME, mascotParameterSet
    2458         .getEnzyme(), fieldsHidden, fieldsDisabled));
    2459     // Maximum missed cleavages
    2460     fs.add( new TextField<String>(
    2461       SaveMascotParameterSetStorage.VMASCOT_MISSED_CLEAVAGES,
    2462       mascotParameterSet.getMissedCleavages(), fieldsHidden,
    2463       fieldsDisabled));
    2464     // Fixed modifications
    2465     fs.add( new TextField<String>(
    2466       SaveMascotParameterSetStorage.VMASCOT_FIXED, mascotParameterSet
    2467         .getFixed(), fieldsHidden, fieldsDisabled));
    2468     // Variable modifications
    2469     fs.add( new TextField<String>(
    2470       SaveMascotParameterSetStorage.VMASCOT_VARIABLE, mascotParameterSet
    2471         .getVariable(), fieldsHidden, fieldsDisabled));
    2472     // Quantitation
    2473     fs.add( new TextField<String>(
    2474       SaveMascotParameterSetStorage.VMASCOT_QUANTITATION,
    2475       mascotParameterSet.getQuantitation(), fieldsHidden,
    2476       fieldsDisabled));
    2477     // Protein mass (kDa)
    2478     fs.add( new TextField<String>(
    2479       SaveMascotParameterSetStorage.VMASCOT_PROTEIN_MASS,
    2480       mascotParameterSet.getProteinMass(), fieldsHidden,
    2481       fieldsDisabled));
    2482     // Peptide mass tolerance
    2483     fs.add( new TextField<String>(
    2484       SaveMascotParameterSetStorage.VMASCOT_PEP_TOL, mascotParameterSet
    2485         .getPepTol(), fieldsHidden, fieldsDisabled));
    2486     // Peptide mass tolerance unit
    2487     fs.add( new TextField<String>(
    2488       SaveMascotParameterSetStorage.VMASCOT_PEP_TOL_UNIT,
    2489       mascotParameterSet.getPepTolUnit(), fieldsHidden,
    2490       fieldsDisabled));
    2491     // Peptide isotope error
    2492     fs.add( new TextField<String>(
    2493       SaveMascotParameterSetStorage.VMASCOT_PEPTIDE_ISOTOPE_ERROR,
    2494       mascotParameterSet.getPeptideIsotopeError(), fieldsHidden,
    2495       fieldsDisabled));
    2496     // MS-MS mass tolerance
    2497     fs.add( new TextField<String>(
    2498       SaveMascotParameterSetStorage.VMASCOT_MSMS_TOL, mascotParameterSet
    2499         .getMsMsTol(), fieldsHidden, fieldsDisabled));
    2500     // MS-MS mass tolerance unit
    2501     fs.add( new TextField<String>(
    2502       SaveMascotParameterSetStorage.VMASCOT_MSMS_TOL_UNIT,
    2503       mascotParameterSet.getMsMsTolUnit(), fieldsHidden,
    2504       fieldsDisabled));
    2505     // Peptide charge
    2506     fs.add( new TextField<String>(
    2507       SaveMascotParameterSetStorage.VMASCOT_PEPTIDE_CHARGE,
    2508       mascotParameterSet.getPeptideCharge(), fieldsHidden,
    2509       fieldsDisabled));
    2510     // Mass ion type
    2511     fs.add( new TextField<String>(
    2512       SaveMascotParameterSetStorage.VMASCOT_MASS_ION_TYPE,
    2513       mascotParameterSet.getMassIonType(), fieldsHidden,
    2514       fieldsDisabled));
    2515     // Mass type
    2516     fs.add( new TextField<String>(
    2517       SaveMascotParameterSetStorage.VMASCOT_MASS_TYPE, mascotParameterSet
    2518         .getMassType(), fieldsHidden, fieldsDisabled));
    2519     // Data format
    2520     fs.add( new TextField<String>(
    2521       SaveMascotParameterSetStorage.VMASCOT_DATA_FORMAT,
    2522       mascotParameterSet.getDataFormat(), fieldsHidden,
    2523       fieldsDisabled));
    2524     // Precursor
    2525     fs.add( new TextField<String>(
    2526       SaveMascotParameterSetStorage.VMASCOT_PRECURSOR, mascotParameterSet
    2527         .getPrecursor(), fieldsHidden, fieldsDisabled));
    2528     // Mascot query
    2529     fs.add( new TextField<String>(
    2530       SaveMascotParameterSetStorage.VMASCOT_MASCOT_QUERY,
    2531       mascotParameterSet.getMascotQuery(), fieldsHidden,
    2532       fieldsDisabled));
    2533     // Instrument
    2534     fs.add( new TextField<String>(
    2535       SaveMascotParameterSetStorage.VMASCOT_INSTRUMENT,
    2536       mascotParameterSet.getInstrument(), fieldsHidden,
    2537       fieldsDisabled));
    2538     // Error tolerant
    2539     fs.add( new TextField<String>(
    2540       SaveMascotParameterSetStorage.VMASCOT_ERROR_TOLERANT,
    2541       mascotParameterSet.getErrorTolerant(), fieldsHidden,
    2542       fieldsDisabled));
    2543     // Decoy
    2544     fs.add( new TextField<String>(
    2545       SaveMascotParameterSetStorage.VMASCOT_DECOY, mascotParameterSet
    2546         .getDecoy(), fieldsHidden, fieldsDisabled));
    2547     // Report top
    2548     fs.add( new TextField<String>(
    2549       SaveMascotParameterSetStorage.VMASCOT_REPORT_TOP,
    2550       mascotParameterSet.getReportTop(), fieldsHidden, fieldsDisabled));
    2551     // Return Fieldset with added fields
    2552     return fs;
    2553   }
     2337 //Cleaning up from here
     2338
    25542339
    25552340
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