Changeset 3863


Ignore:
Timestamp:
Sep 20, 2010, 11:05:42 AM (13 years ago)
Author:
Gregory Vincic
Message:

Refs #698. Removed method getMascotParameterSetForm from FormFactory.

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

Legend:

Unmodified
Added
Removed

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

    r3825 r3863  
    197197    reportTopOptionList = stringListToOptionList(reportTopStringList);
    198198    // Mascot parameter set form
    199     mascotParameterSetForm = getFormFactory().getMascotParameterSetForm(mascotParameterSet,
     199    mascotParameterSetForm = new MascotStorageForm(mascotParameterSet,
    200200      enzymeOptionList,
    201201      missedCleavagesOptionList,

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

    r3862 r3863  
    22872287
    22882288
    2289   /**
    2290    * Returns a select box for selecting a list of string values.
    2291    *
    2292    * @param validParam VString Valid VString parameter coupled to select box.
    2293    * @param optionList List<Option> Option list of options.
    2294    * @param selected List<String> List with values of selected options.
    2295    * @return Select<VString> A select box for selecting a string value.
    2296    */
    2297   private Select<VString> newStringMultipleSelectBox(VString validParam,
    2298       List<Option> optionList, List<String> selectedList)
    2299   {
    2300     Select<VString> select = new Select<VString>(validParam);
    2301     select.setLabel(validParam.getName());
    2302     // Add options in list order
    2303     if (optionList != null)
    2304     {
    2305       for (int i = 0; i < optionList.size(); i++)
    2306       {
    2307         if (optionList.get(i) != null)
    2308         {
    2309           select.addOption(optionList.get(i));
    2310         }
    2311       }
    2312     }
    2313     // Set selected options
    2314     if (selectedList != null)
    2315     {
    2316       if (select.getOptions() != null)
    2317       {
    2318         for (int i = 0; i < select.getOptions().size(); i++)
    2319         {
    2320           // Check all selected options in list
    2321           for (int j = 0; j < selectedList.size(); j++)
    2322           {
    2323             if (select.getOptions().get(i).getValue().equals(
    2324               selectedList.get(j)))
    2325             {
    2326               select.getOptions().get(i).setSelected(true);
    2327             }
    2328           }
    2329         }
    2330       }
    2331     }
    2332     // Set default visible number of options
    2333     select.setMaxSize(5);
    2334     return select;
    2335   }
    2336 
    23372289 //Cleaning up from here
    2338 
    2339 
    2340   public Form getMascotParameterSetForm(
    2341       MascotParameterSet mascotParameterSet,
    2342       List<Option> enzymeOptionList,
    2343       List<Option> missedCleavagesOptionList,
    2344       List<Option> sequenceLibraryOptionList,
    2345       List<Option> speciesOptionList, List<Option> fixedModsOptionList,
    2346       List<Option> variableModsOptionList,
    2347       List<Option> quantitationOptionList,
    2348       List<Option> peptideTolUnitOptionList,
    2349       List<Option> peptideIsotopeErrorOptionList,
    2350       List<Option> msMsTolUnitOptionList,
    2351       List<Option> peptideChargeOptionList,
    2352       List<Option> dataFormatOptionList,
    2353       List<Option> instrumentOptionList, List<Option> reportTopOptionList)
    2354   {
    2355     //
    2356     MascotParameterFileUtil mascotParameterFileUtil = new MascotParameterFileUtil();
    2357     // String delimRegex = new String(",\\ ");
    2358     String delimRegex = new String(",");
    2359     // Fetch help hash tables to find attribute strings
    2360     Hashtable<String, String> searchTypeHT = mascotParameterFileUtil
    2361       .fetchSearchTypeAttributeHashtable();
    2362     Hashtable<String, String> massIonTypeHT = mascotParameterFileUtil
    2363       .fetchMassIonTypeAttributeHashtable();
    2364     List<String> searchTypeL = mascotParameterFileUtil
    2365       .fetchSearchTypeAlternativesList();
    2366     List<String> enzymeL = mascotParameterFileUtil
    2367       .fetchEnzymeAlternativesList();
    2368     List<String> missedCleavagesL = mascotParameterFileUtil
    2369       .fetchMissedCleavagesAlternativesList();
    2370     List<String> sequenceLibraryL = mascotParameterFileUtil
    2371       .fetchSequenceLibraryAlternativesList();
    2372     List<String> speciesL = mascotParameterFileUtil
    2373       .fetchSpeciesAlternativesList();
    2374     List<String> modificationL = mascotParameterFileUtil
    2375       .fetchModificationAlternativesList();
    2376     List<String> quantitationL = mascotParameterFileUtil
    2377       .fetchQuantitationAlternativesList();
    2378     List<String> peptideTolUnitL = mascotParameterFileUtil
    2379       .fetchPeptideTolUnitAlternativesList();
    2380     List<String> peptideIsotopeErrorL = mascotParameterFileUtil
    2381       .fetchPeptideIsotopeErrorAlternativesList();
    2382     List<String> msMsTolUnitL = mascotParameterFileUtil
    2383       .fetchMsMsTolUnitAlternativesList();
    2384     List<String> peptideChargeL = mascotParameterFileUtil
    2385       .fetchPeptideChargeAlternativesList();
    2386     List<String> massIonTypeL = mascotParameterFileUtil
    2387       .fetchMassIonTypeAlternativesList();
    2388     List<String> massTypeL = mascotParameterFileUtil
    2389       .fetchMassTypeAlternativesList();
    2390     List<String> dataFormatL = mascotParameterFileUtil
    2391       .fetchDataFormatAlternativesList();
    2392     List<String> instrumentL = mascotParameterFileUtil
    2393       .fetchInstrumentAlternativesList();
    2394     List<String> reportTopL = mascotParameterFileUtil
    2395       .fetchReportTopAlternativesList();
    2396     // DbControl dc = project.getDbControl();
    2397     Form form = new Form("MascotParameterSetForm");
    2398     /*
    2399      * String select box variables
    2400      */
    2401     VString validStringParam = null;
    2402     List<String> stringList = null;
    2403     List<Option> optionList = null;
    2404     String selected = null;
    2405     List<String> selectedList = null;
    2406     /*
    2407      * General field set
    2408      */
    2409     Fieldset generalFS = new Fieldset();
    2410     // Make sure that search type is one of "MIS" (default), "SQ", "PMF"
    2411     String searchTypeInput = mascotParameterSet.getSearchType();
    2412     if (searchTypeInput == null)
    2413     {
    2414       searchTypeInput = new String("MIS");
    2415     }
    2416     else if (!searchTypeInput.equals("MIS") && !searchTypeInput
    2417       .equals("SQ") && !searchTypeInput.equals("PMF"))
    2418     {
    2419       searchTypeInput = new String("MIS");
    2420     }
    2421     // Get field set legend title
    2422     String generalFSTitle = new String("MascotParameterSetGeneral");
    2423     if (searchTypeInput.equals("MIS"))
    2424     {
    2425       generalFSTitle = new String("MascotParameterSetGeneralMIS");
    2426     }
    2427     else if (searchTypeInput.equals("SQ"))
    2428     {
    2429       generalFSTitle = new String("MascotParameterSetGeneralSQ");
    2430     }
    2431     else if (searchTypeInput.equals("PMF"))
    2432     {
    2433       generalFSTitle = new String("MascotParameterSetGeneralPMF");
    2434     }
    2435    
    2436     generalFS.setTitle(generalFSTitle);
    2437     form.addFieldset(generalFS);
    2438     //
    2439     // General, search type
    2440     // Parameter value fixed and only shown via field set title,
    2441     // but transmitted via hidden field.
    2442     TextField<String> searchTypeF = new TextField<String>(SaveMascotParameterSetStorage.VMASCOT_SEARCH_TYPE);
    2443     searchTypeF.setValue(searchTypeInput);
    2444     searchTypeF.setHidden(true);
    2445     generalFS.add(searchTypeF);
    2446     //
    2447     // General, search title
    2448     TextField<String> searchTitleF = new TextField<String>(SaveMascotParameterSetStorage.VMASCOT_SEARCH_TITLE);
    2449     searchTitleF.setValue(mascotParameterSet.getSearchTitle());
    2450     searchTitleF.setLabel("MascotSearchTitle");
    2451     generalFS.add(searchTitleF);
    2452     //
    2453     // General, sequence library
    2454     validStringParam = SaveMascotParameterSetStorage.VMASCOT_DB;
    2455     optionList = new ArrayList<Option>();
    2456     for (String key : sequenceLibraryL)
    2457     {
    2458       optionList.add(new Option(key, key));
    2459     }
    2460     // Use input sequence library option list if present
    2461     if (sequenceLibraryOptionList != null && sequenceLibraryOptionList
    2462       .size() > 0)
    2463     {
    2464       optionList = sequenceLibraryOptionList;
    2465     }
    2466     selected = mascotParameterSet.getDb();
    2467     Select<VString> sequenceLibrarySelectBox = new Select<VString>(validStringParam, optionList);
    2468    sequenceLibrarySelectBox.selectOption(selected);
    2469     sequenceLibrarySelectBox.setLabel("MascotSequenceLibrarySelect");
    2470     generalFS.add(sequenceLibrarySelectBox);
    2471     //
    2472     // General, species
    2473     validStringParam = SaveMascotParameterSetStorage.VMASCOT_SPECIES;
    2474     optionList = new ArrayList<Option>();
    2475     for (String key : speciesL)
    2476     {
    2477       // optionList.add(new Option(key, speciesHT.get(key)));
    2478       optionList.add(new Option(key, key));
    2479     }
    2480     // Use input species option list if present
    2481     if (speciesOptionList != null && speciesOptionList.size() > 0)
    2482     {
    2483       optionList = speciesOptionList;
    2484     }
    2485     selected = mascotParameterSet.getSpecies();
    2486     Select<VString> speciesSelectBox = new Select<VString>(validStringParam, optionList);
    2487   speciesSelectBox.selectOption(selected);
    2488     speciesSelectBox.setLabel("MascotSpecies");
    2489     generalFS.add(speciesSelectBox);
    2490     //
    2491     // General, enzyme
    2492     validStringParam = SaveMascotParameterSetStorage.VMASCOT_ENZYME;
    2493     optionList = new ArrayList<Option>();
    2494     for (String key : enzymeL)
    2495     {
    2496       // optionList.add(new Option(key, enzymeHT.get(key)));
    2497       optionList.add(new Option(key, key));
    2498     }
    2499     // Use input enzyme option list if present
    2500     if (enzymeOptionList != null && enzymeOptionList.size() > 0)
    2501     {
    2502       optionList = enzymeOptionList;
    2503     }
    2504     selected = mascotParameterSet.getEnzyme();
    2505     Select<VString> enzymeSelectBox = new Select<VString>(validStringParam, optionList);
    2506   enzymeSelectBox.selectOption(selected);
    2507     enzymeSelectBox.setLabel("MascotEnzymeSelect");
    2508     generalFS.add(enzymeSelectBox);
    2509     //
    2510     // General, missed cleavages
    2511     validStringParam = SaveMascotParameterSetStorage.VMASCOT_MISSED_CLEAVAGES;
    2512     optionList = new ArrayList<Option>();
    2513     for (String key : missedCleavagesL)
    2514     {
    2515       optionList.add(new Option(key, key));
    2516     }
    2517     // Use input missed cleavages option list if present
    2518     if (missedCleavagesOptionList != null && missedCleavagesOptionList
    2519       .size() > 0)
    2520     {
    2521       optionList = missedCleavagesOptionList;
    2522     }
    2523     selected = mascotParameterSet.getMissedCleavages();
    2524     Select<VString> missedCleavagesSelectBox = new Select<VString>(validStringParam, optionList);
    2525   missedCleavagesSelectBox.selectOption(selected);
    2526     missedCleavagesSelectBox.setLabel("MascotMissedCleavagesSelect");
    2527     generalFS.add(missedCleavagesSelectBox);
    2528     // Fixed mods
    2529     validStringParam = SaveMascotParameterSetStorage.VMASCOT_FIXED;
    2530     optionList = new ArrayList<Option>();
    2531     for (String key : modificationL)
    2532     {
    2533       // optionList.add(new Option(key, modificationHT.get(key)));
    2534       optionList.add(new Option(key, key));
    2535     }
    2536     // Use input fixed mods option list if present
    2537     if (fixedModsOptionList != null && fixedModsOptionList.size() > 0)
    2538     {
    2539       optionList = fixedModsOptionList;
    2540     }
    2541     selected = mascotParameterSet.getFixed();
    2542     selectedList = listStringToStringList(selected, delimRegex);
    2543     Select<VString> fixedMods = newStringMultipleSelectBox(validStringParam, optionList, selectedList);
    2544     fixedMods.setLabel("MascotFixedMods");
    2545     fixedMods.setMultiple(true);
    2546     fixedMods.setSize(5);
    2547     generalFS.add(fixedMods);
    2548     // Variable mods
    2549     validStringParam = SaveMascotParameterSetStorage.VMASCOT_VARIABLE;
    2550     optionList = new ArrayList<Option>();
    2551     for (String key : modificationL)
    2552     {
    2553       // optionList.add(new Option(key, modificationHT.get(key)));
    2554       optionList.add(new Option(key, key));
    2555     }
    2556     // Use input varible mods option list if present
    2557     if (variableModsOptionList != null && variableModsOptionList.size() > 0)
    2558     {
    2559       optionList = variableModsOptionList;
    2560     }
    2561     selected = mascotParameterSet.getVariable();
    2562     selectedList = listStringToStringList(selected, delimRegex);
    2563     Select<VString> variableMods = newStringMultipleSelectBox(
    2564       validStringParam, optionList, selectedList);
    2565     variableMods.setLabel("MascotVariableMods");
    2566     variableMods.setMultiple(true);
    2567     variableMods.setSize(5);
    2568     generalFS.add(variableMods);
    2569     if (searchTypeInput.equals("MIS") || searchTypeInput.equals("SQ"))
    2570     {
    2571       // General, quantitation
    2572       validStringParam = SaveMascotParameterSetStorage.VMASCOT_QUANTITATION;
    2573       optionList = new ArrayList<Option>();
    2574       for (String key : quantitationL)
    2575       {
    2576         optionList.add(new Option(key, key));
    2577       }
    2578       // Use input quantitation option list if present
    2579       if (quantitationOptionList != null && quantitationOptionList.size() > 0)
    2580       {
    2581         optionList = quantitationOptionList;
    2582       }
    2583       selected = mascotParameterSet.getQuantitation();
    2584       Select<VString> quantitationSelectBox = new Select<VString>(validStringParam, optionList);
    2585     quantitationSelectBox.selectOption(selected);
    2586       quantitationSelectBox.setLabel("MascotQuantitationSelect");
    2587       generalFS.add(quantitationSelectBox);
    2588     }
    2589     if (searchTypeInput.equals("PMF"))
    2590     {
    2591       // General, protein mass (kDa)
    2592       TextField<String> proteinMassF = new TextField<String>(SaveMascotParameterSetStorage.VMASCOT_PROTEIN_MASS);
    2593       proteinMassF.setValue(mascotParameterSet.getProteinMass());
    2594       generalFS.add(proteinMassF);
    2595     }
    2596 
    2597     // General, peptide mass tolerance
    2598     TextField<String> peptideMassToleranceF = new TextField<String>(SaveMascotParameterSetStorage.VMASCOT_PEP_TOL);
    2599     peptideMassToleranceF.setValue(mascotParameterSet.getPepTol());
    2600     generalFS.add(peptideMassToleranceF);
    2601 
    2602     // General, peptide mass tolerance unit
    2603     validStringParam = SaveMascotParameterSetStorage.VMASCOT_PEP_TOL_UNIT;
    2604     optionList = new ArrayList<Option>();
    2605     for (String key : peptideTolUnitL)
    2606     {
    2607       optionList.add(new Option(key, key));
    2608     }
    2609     // Use input peptide tolerance unit option list if present
    2610     if (peptideTolUnitOptionList != null && peptideTolUnitOptionList.size() > 0)
    2611     {
    2612       optionList = peptideTolUnitOptionList;
    2613     }
    2614     selected = mascotParameterSet.getPepTolUnit();
    2615     Select<VString> peptideTolUnitSelectBox = new Select<VString>(validStringParam, optionList);
    2616   peptideTolUnitSelectBox.selectOption(selected);
    2617     peptideTolUnitSelectBox.setLabel("MascotPeptideToleranceUnitSelect");
    2618     generalFS.add(peptideTolUnitSelectBox);
    2619     if (searchTypeInput.equals("MIS"))
    2620     {
    2621 
    2622       // General, peptide isotope error
    2623       validStringParam = SaveMascotParameterSetStorage.VMASCOT_PEPTIDE_ISOTOPE_ERROR;
    2624       optionList = new ArrayList<Option>();
    2625       for (String key : peptideIsotopeErrorL)
    2626       {
    2627         optionList.add(new Option(key, key));
    2628       }
    2629       // Use input peptide isotope error option list if present
    2630       if (peptideIsotopeErrorOptionList != null && peptideIsotopeErrorOptionList
    2631         .size() > 0)
    2632       {
    2633         optionList = peptideIsotopeErrorOptionList;
    2634       }
    2635       selected = mascotParameterSet.getPeptideIsotopeError();
    2636       Select<VString> peptideIsotopeErrorSelectBox = new Select<VString>(
    2637         validStringParam, optionList);
    2638   peptideIsotopeErrorSelectBox.selectOption( selected);
    2639       peptideIsotopeErrorSelectBox
    2640         .setLabel("MascotPeptideIsotopeErrorSelect");
    2641       generalFS.add(peptideIsotopeErrorSelectBox);
    2642     }
    2643     if (searchTypeInput.equals("MIS") || searchTypeInput.equals("SQ"))
    2644     {
    2645       // General, MS/MS mass tolerance
    2646       TextField<String> msMsMassToleranceF = new TextField<String>(SaveMascotParameterSetStorage.VMASCOT_MSMS_TOL);
    2647       msMsMassToleranceF.setValue(mascotParameterSet.getMsMsTol());
    2648       generalFS.add(msMsMassToleranceF);
    2649       // General, MS/MS mass tolerance unit
    2650       validStringParam = SaveMascotParameterSetStorage.VMASCOT_MSMS_TOL_UNIT;
    2651       optionList = new ArrayList<Option>();
    2652       for (String key : msMsTolUnitL)
    2653       {
    2654         optionList.add(new Option(key, key));
    2655       }
    2656       // Use input MS/MS tolerance unit option list if present
    2657       if (msMsTolUnitOptionList != null && msMsTolUnitOptionList.size() > 0)
    2658       {
    2659         optionList = msMsTolUnitOptionList;
    2660       }
    2661       selected = mascotParameterSet.getMsMsTolUnit();
    2662       Select<VString> msMsTolUnitSelectBox = new Select<VString>(
    2663         validStringParam, optionList);
    2664   msMsTolUnitSelectBox.selectOption( selected);
    2665       msMsTolUnitSelectBox.setLabel("MascotMsMsToleranceUnitSelect");
    2666       generalFS.add(msMsTolUnitSelectBox);
    2667       //
    2668       // General, peptide charge
    2669       validStringParam = SaveMascotParameterSetStorage.VMASCOT_PEPTIDE_CHARGE;
    2670       optionList = new ArrayList<Option>();
    2671       for (String key : peptideChargeL)
    2672       {
    2673         optionList.add(new Option(key, key));
    2674       }
    2675       // Use input peptide charge option list if present
    2676       if (peptideChargeOptionList != null && peptideChargeOptionList
    2677         .size() > 0)
    2678       {
    2679         optionList = peptideChargeOptionList;
    2680       }
    2681       selected = mascotParameterSet.getPeptideCharge();
    2682       Select<VString> peptideChargeSelectBox = new Select<VString>(
    2683         validStringParam, optionList);
    2684   peptideChargeSelectBox.selectOption( selected);
    2685       peptideChargeSelectBox.setLabel("MascotPeptideChargeSelect");
    2686       generalFS.add(peptideChargeSelectBox);
    2687     }
    2688     if (searchTypeInput.equals("PMF"))
    2689     {
    2690       //
    2691       // General, mass ion type
    2692       validStringParam = SaveMascotParameterSetStorage.VMASCOT_MASS_ION_TYPE;
    2693       optionList = new ArrayList<Option>();
    2694       for (String key : massIonTypeL)
    2695       {
    2696         optionList.add(new Option(key, massIonTypeHT.get(key)));
    2697       }
    2698       selected = mascotParameterSet.getMassIonType();
    2699       Select<VString> massIonTypeSelectBox = new Select<VString>(
    2700         validStringParam, optionList);
    2701   massIonTypeSelectBox.selectOption( selected);
    2702       massIonTypeSelectBox.setLabel("MascotMassIonTypeSelect");
    2703       generalFS.add(massIonTypeSelectBox);
    2704     }
    2705     //
    2706     // General, mass type
    2707     validStringParam = SaveMascotParameterSetStorage.VMASCOT_MASS_TYPE;
    2708     optionList = new ArrayList<Option>();
    2709     for (String key : massTypeL)
    2710     {
    2711       optionList.add(new Option(key, key));
    2712     }
    2713     selected = mascotParameterSet.getMassType();
    2714     Select<VString> massTypeSelectBox = new Select<VString>(
    2715       validStringParam, optionList);
    2716   massTypeSelectBox.selectOption( selected);
    2717     massTypeSelectBox.setLabel("MascotMassTypeSelect");
    2718     generalFS.add(massTypeSelectBox);
    2719     if (searchTypeInput.equals("MIS"))
    2720     {
    2721       // General, data format
    2722       validStringParam = SaveMascotParameterSetStorage.VMASCOT_DATA_FORMAT;
    2723       optionList = new ArrayList<Option>();
    2724       for (String key : dataFormatL)
    2725       {
    2726         optionList.add(new Option(key, key));
    2727       }
    2728       // Use input data format list if present
    2729       if (dataFormatOptionList != null && dataFormatOptionList.size() > 0)
    2730       {
    2731         optionList = dataFormatOptionList;
    2732       }
    2733       selected = mascotParameterSet.getDataFormat();
    2734       Select<VString> dataFormatSelectBox = new Select<VString>(
    2735         validStringParam, optionList);
    2736   dataFormatSelectBox.selectOption( selected);
    2737       dataFormatSelectBox.setLabel("MascotDataFormatSelect");
    2738       generalFS.add(dataFormatSelectBox);
    2739       //
    2740       // General, precursor
    2741       TextField<String> precursorF = new TextField<String>(SaveMascotParameterSetStorage.VMASCOT_PRECURSOR);
    2742       precursorF.setValue(mascotParameterSet.getPrecursor());
    2743       precursorF.setLabel("MascotPrecursor");
    2744       generalFS.add(precursorF);
    2745     }
    2746     if (searchTypeInput.equals("SQ") || searchTypeInput.equals("PMF"))
    2747     {
    2748       // General, Mascot query
    2749       TextArea mascotQueryF = new TextArea(
    2750         SaveMascotParameterSetStorage.VMASCOT_MASCOT_QUERY);
    2751       mascotQueryF.setValue(mascotParameterSet.getMascotQuery());
    2752       mascotQueryF.setLabel("MascotMascotQuery");
    2753       generalFS.add(mascotQueryF);
    2754     }
    2755     if (searchTypeInput.equals("MIS") || searchTypeInput.equals("SQ"))
    2756     {
    2757       // General, instrument
    2758       validStringParam = SaveMascotParameterSetStorage.VMASCOT_INSTRUMENT;
    2759       optionList = new ArrayList<Option>();
    2760       for (String key : instrumentL)
    2761       {
    2762         optionList.add(new Option(key, key));
    2763       }
    2764       // Use input instrument list if present
    2765       if (instrumentOptionList != null && instrumentOptionList.size() > 0)
    2766       {
    2767         optionList = instrumentOptionList;
    2768       }
    2769       selected = mascotParameterSet.getInstrument();
    2770       Select<VString> instrumentSelectBox = new Select<VString>(validStringParam, optionList);
    2771   instrumentSelectBox.selectOption( selected);
    2772       instrumentSelectBox.setLabel("MascotInstrumentSelect");
    2773       generalFS.add(instrumentSelectBox);
    2774     }
    2775     if (searchTypeInput.equals("MIS"))
    2776     {
    2777       // General, error tolerant
    2778       Checkbox<VString> errorTolerantCB = new Checkbox<VString>(
    2779         SaveMascotParameterSetStorage.VMASCOT_ERROR_TOLERANT);
    2780       errorTolerantCB.setLabel("MascotErrorTolerantSelect");
    2781       errorTolerantCB.setValue("1");
    2782       selected = mascotParameterSet.getErrorTolerant();
    2783       errorTolerantCB.isChecked(false);
    2784       if (selected != null && selected.equals("1"))
    2785       {
    2786         errorTolerantCB.isChecked(true);
    2787       }
    2788       generalFS.add(errorTolerantCB);
    2789     }
    2790     // General, decoy
    2791     Checkbox<VString> decoyCB = new Checkbox<VString>(
    2792       SaveMascotParameterSetStorage.VMASCOT_DECOY);
    2793     decoyCB.setLabel("MascotDecoySelect");
    2794     decoyCB.setValue("1");
    2795     selected = mascotParameterSet.getDecoy();
    2796     decoyCB.isChecked(false);
    2797     if (selected != null && selected.equals("1"))
    2798     {
    2799       decoyCB.isChecked(true);
    2800     }
    2801     generalFS.add(decoyCB);
    2802     // General, report top
    2803     validStringParam = SaveMascotParameterSetStorage.VMASCOT_REPORT_TOP;
    2804     optionList = new ArrayList<Option>();
    2805     for (String key : reportTopL)
    2806     {
    2807       optionList.add(new Option(key, key));
    2808     }
    2809     // Use input report top list if present
    2810     if (reportTopOptionList != null && reportTopOptionList.size() > 0)
    2811     {
    2812       optionList = reportTopOptionList;
    2813     }
    2814     selected = mascotParameterSet.getReportTop();
    2815     Select<VString> reportTopSelectBox = new Select<VString>(validStringParam, optionList);
    2816   reportTopSelectBox.selectOption( selected);
    2817     reportTopSelectBox.setLabel("MascotReportTopSelect");
    2818     generalFS.add(reportTopSelectBox);
    2819     return form;
    2820   }
    28212290
    28222291
    … …  
    32232692    selected = omssaParameterSet.getSpecies();
    32242693    selectedList = listStringToStringList(selected, delimRegex);
    3225     Select<VString> species = newStringMultipleSelectBox(validStringParam,
     2694    Select<VString> species = new Select<VString>(validStringParam,
    32262695      optionList, selectedList);
    32272696    species.setLabel("OMSSASpecies");
    … …  
    32582727    selected = omssaParameterSet.getFixed();
    32592728    selectedList = listStringToStringList(selected, delimRegex);
    3260     Select<VString> fixedMods = newStringMultipleSelectBox(validStringParam, optionList, selectedList);
     2729    Select<VString> fixedMods = new Select<VString>(validStringParam, optionList, selectedList);
    32612730    fixedMods.setLabel("OMSSAFixedMods");
    32622731    fixedMods.setMultiple(true);
    … …  
    32832752    selected = omssaParameterSet.getVariable();
    32842753    selectedList = listStringToStringList(selected, delimRegex);
    3285     Select<VString> variableMods = newStringMultipleSelectBox(
     2754    Select<VString> variableMods = new Select<VString>(
    32862755      validStringParam, optionList, selectedList);
    32872756    variableMods.setLabel("OMSSAVariableMods");
    … …  
    46224091    log
    46234092      .debug("residue potential modification mass selectedList = " + selectedList);
    4624     Select<VString> residuePotentialModificationMassSelectBox = newStringMultipleSelectBox(
     4093    Select<VString> residuePotentialModificationMassSelectBox = new Select<VString>(
    46254094      validStringParam, optionList, selectedList);
    46264095    residuePotentialModificationMassSelectBox
    … …  
    47014170    selected = xTandemParameterSet.getProteinTaxon();
    47024171    selectedList = listStringToStringList(selected, ",\\ ");
    4703     Select<VString> taxon = newStringMultipleSelectBox(validStringParam,
     4172    Select<VString> taxon = new Select<VString>(validStringParam,
    47044173      optionList, selectedList);
    47054174    taxon.setLabel("XTandemProteinTaxonEukaryotes");
    … …  
    47454214    }
    47464215    // Same selection list as for Eukaryotes taxon is used for Prokaryotes
    4747     Select<VString> taxon1 = newStringMultipleSelectBox(validStringParam,
     4216    Select<VString> taxon1 = new Select<VString>(validStringParam,
    47484217      optionList, selectedList);
    47494218    taxon1.setLabel("XTandemProteinTaxonProkaryotes");
    … …  
    49284397    log
    49294398      .debug("refine potential modification mass selectedList = " + selectedList);
    4930     Select<VString> refinePotentialModificationMassSelectBox = newStringMultipleSelectBox(
     4399    Select<VString> refinePotentialModificationMassSelectBox = new Select<VString>(
    49314400      validStringParam, optionList, selectedList);
    49324401    refinePotentialModificationMassSelectBox
    … …  
    52674736    }
    52684737    selectedList = pikeFieldSelectList;
    5269     Select<VString> fieldSelect = newStringMultipleSelectBox(
     4738    Select<VString> fieldSelect = new Select<VString>(
    52704739      validStringParam, optionList, selectedList);
    52714740    fieldSelect.setLabel("PIKEFieldSelect");
    … …  
    53274796    }
    53284797    selectedList = pikeOutputFileTypeList;
    5329     Select<VString> outputFileTypeSelect = newStringMultipleSelectBox(
     4798    Select<VString> outputFileTypeSelect = new Select<VString>(
    53304799      validStringParam, optionList, selectedList);
    53314800    outputFileTypeSelect.setLabel("PIKEOutputFileTypeSelect");

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

    r3856 r3863  
    3333
    3434/**
    35  * Cell within a table.
    36  *
    3735 * @author gregory
    3836 */
    … …  
    5957  {
    6058    this(param); 
    61   this.options = options;
     59  this.options.addAll(options);
    6260  }
    6361
    … …  
    6765  for(String str : options)
    6866  {
    69    Option opt = new Option(str);   
    70    addOption(opt);   
     67    Option o = new Option(str);
     68    addOption(o);
    7169  }
    7270  selectOption(selected);
    7371  }
     72
     73 public Select(D param ,  List<Option> optionList, List<String> selected)
     74 {
     75  this(param);
     76  this.options.addAll(options);
     77  for(String str : selected)
     78  {
     79   selectOption(str);
     80  }
     81  setMaxSize(5); 
     82 }
    7483
    7584  public String getName()
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