Changeset 3866


Ignore:
Timestamp:
Sep 23, 2010, 8:36:33 AM (13 years ago)
Author:
Gregory Vincic
Message:

Refs #698. Removed method getSaveAsOMSSAParameterSetStorageForm from FormFactory. Decided to put this form creation within the action class that uses it.

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

Legend:

Unmodified
Added
Removed
  • trunk/client/servlet/src/org/proteios/action/omssa/SaveOMSSAParameterSetStorage.java

    r3828 r3866  
    236236        log.debug("omssapss.getParameterFile() = \"" + omssapss.getParameterFile() + "\"");
    237237        // OMSSAParameterSetStorage form
    238         //Form form = getFormFactory().getSaveAsOMSSAParameterSetStorageForm(omssaParameterSetStorage, omssaParameterSet);
    239         Form form = getFormFactory().getSaveAsOMSSAParameterSetStorageForm(omssapss, omssaParameterSet);
     238        Form form = getSaveAsOMSSAParameterSetStorageForm(omssapss, omssaParameterSet);
    240239        // Toolbar
    241240        Toolbar tb = new Toolbar();
     
    757756  }
    758757
     758
     759  public Form getSaveAsOMSSAParameterSetStorageForm(
     760      OMSSAParameterSetStorage omssaParameterSetStorage,
     761      OMSSAParameterSet obj)
     762  {
     763    Form form = new Form("SaveAsOMSSAParameterSetStorage");
     764    form.setTitle("SaveAsOMSSAParameterSetStorage");
     765    Fieldset fs = new Fieldset("SaveAsOMSSAParameterSetStorage");
     766    // OMSSAParameterSetStorage Name
     767    TextField<String> nameF = new NameField();
     768    fs.add(nameF);
     769    nameF.setValue("OMSSA parameter set storage");
     770
     771    // OMSSAParameterSetStorage Description
     772    TextArea descF = new DescriptionField();
     773    fs.add(descF);
     774    descF.setValue("OMSSA parameter set storage");
     775
     776    // OMSSA Parameters Template File
     777    TextField<String> parameterFileF = new FileNameField();
     778    fs.add(parameterFileF);
     779    parameterFileF.setLabel("OMSSAParameterTemplateFile");
     780    parameterFileF.setValue(getLocale().get("NotSpecifiedDefaultUsed"));
     781    parameterFileF.setDisabled(true);
     782
     783    // OMSSA Parameters Template File id
     784    TextField<Integer> parameterFileIdF = new TextField<Integer>(AddOMSSAParameterSetStorage.VOMSSAPARAMETERTEMPLATEFILEID);
     785    fs.add(parameterFileIdF);
     786    parameterFileIdF.setHidden(true);
     787    parameterFileIdF.setLabel("OMSSAParameterTemplateFileId");
     788    parameterFileIdF.setValue(0);
     789
     790    // Hidden text field for initial omssaParameterSetStorage id
     791    TextField<Integer> iniOMSSApssIdF = new TextField<Integer>(
     792      ViewActiveOMSSAParameterSetStorage.VOMSSAPARAMETERSETSTORAGEID);
     793    iniOMSSApssIdF.setHidden(true);
     794    if (omssaParameterSetStorage != null)
     795    {
     796      nameF.setValue(omssaParameterSetStorage.getName());
     797      descF.setValue(omssaParameterSetStorage.getDescription());
     798      iniOMSSApssIdF.setValue(omssaParameterSetStorage.getId());
     799    if (omssaParameterSetStorage.getParameterFile() != null)
     800      {
     801        parameterFileIdF.setValue(omssaParameterSetStorage.getParameterFile().getId());
     802        parameterFileF.setValue(omssaParameterSetStorage.getParameterFile().getPath().toString());
     803      }
     804    }
     805    fs.add(iniOMSSApssIdF);
     806    // Hidden text fields for transferring values of OMSSA parameter set
     807  List<TextField> fields = new ArrayList<TextField>(51);
     808    // Species (taxon)
     809    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SPECIES, obj.getSpecies()));
     810    // Search spectrum type
     811    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_SPECTRUM_TYPE, obj.getSearchSpectrumType()));
     812    // Precursor ion search type
     813    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_SEARCH_TYPE,  obj.getPrecursorSearchType()));
     814    // Product ion search type
     815    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRODUCT_SEARCH_TYPE,  obj.getProductSearchType()));
     816    // Ions to search 1
     817    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_1, obj.getIonsToSearch1()));
     818    // Ions to search 2
     819    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_2, obj.getIonsToSearch2()));
     820    // Precursor mass tolerance (Da)
     821    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PEP_TOL, obj.getPepTol()));
     822    // Product mass tolerance (Da)
     823    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MSMS_TOL, obj.getMsMsTol()));
     824    // Charge dependency of precursor mass tolerance (0 = none, 1 = linear)
     825    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_ZDEP, obj.getZDep()));
     826    // E-value cutoff
     827    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTOFF, obj.getCutoff()));
     828    // Peak low intensity cutoff (fraction of most intense)
     829    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTLO, obj.getCutLo()));
     830    // Peak high intensity cutoff (fraction of most intense)
     831    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTHI, obj.getCutHi()));
     832    // Peak intensity cutoff increment (fraction of most intense)
     833    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTINC, obj.getCutInc()));
     834    // Single charge window in Da
     835    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_WIN, obj.getSingleWin()));
     836    // Double charge window in Da
     837    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_WIN, obj.getDoubleWin()));
     838    // Number of peaks allowed in single charge window
     839    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_NUM, obj.getSingleNum()));
     840    // Number of peaks allowed in double charge window
     841    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_NUM, obj.getDoubleNum()));
     842    // Fixed modifications
     843    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_FIXED, obj.getFixed()));
     844    // Variable modifications
     845    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_VARIABLE, obj.getVariable()));
     846    // Enzyme
     847    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_ENZYME, obj.getEnzyme()));
     848    // Maximum missed cleavages
     849    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MISSED_CLEAVE,  obj.getMissedCleave()));
     850    // Hit list max length
     851    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_HIT_LIST_LEN, obj.getHitListLen()));
     852    // Sequence library
     853    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DB, obj.getDb()));
     854    // Number of top intensity peaks in first pass
     855    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_TOP_HIT_NUM, obj.getTopHitNum()));
     856    // Minimum number of m/z matches a sequence library peptide must have
     857    // for the hit to the peptide to be recorded
     858    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_HIT, obj.getMinHit()));
     859    // Minimum number of m/z values a spectrum must have to be searched
     860    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_SPECTRA, obj.getMinSpectra()));
     861    // Scale
     862    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SCALE, obj.getScale()));
     863    // Maximum variable mod combinations searched per peptide
     864    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_MODS, obj.getMaxMods()));
     865    // Should charge plus one be determined algorithmically? (1=yes)
     866    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_PLUS_ONE, obj.getMsCalcPlusOne()));
     867    // How should precursor charges be determined? (1=believe the input
     868    // file, 2=use a range)
     869    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_CHARGE, obj.getMsCalcCharge()));
     870    // Minimum precursor charge to search when not 1+
     871    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_CHARGE, obj.getMinCharge()));
     872    // Maximum precursor charge to search when not 1+
     873    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_CHARGE, obj.getMaxCharge()));
     874    // Minimum charge to start using multiply charged products
     875    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CONSIDER_MULT,  obj.getConsiderMult()));
     876    // Fraction of product peaks below precursor to determine +1 precursor
     877    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PLUS_ONE, obj.getPlusOne()));
     878    // Maximum product charge to search
     879    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCT_CHARGE, obj.getMaxProductCharge()));
     880    // Minimum number of precursors that match a spectrum
     881    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PSEUDO_COUNT, obj.getPseudoCount()));
     882    // Should first forward (b1) product ions be in search (1=no)
     883    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_B1, obj.getSearchB1()));
     884    // Should C terminus ions be searched (1=no)
     885    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_C_TERM_PRODUCT,  obj.getSearchCTermProduct()));
     886    // Max number of ions in each series being searched (0=all)
     887    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCTIONS,  obj.getMaxProductions()));
     888    // Minimum size of peptides for no-enzyme and semi-tryptic searches
     889    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_NO_ENZYME,  obj.getMinNoEnzyme()));
     890    // Maximum size of peptides for no-enzyme and semi-tryptic searches
     891    // (0=none)
     892    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_NO_ENZYME,  obj.getMaxNoEnzyme()));
     893    // Threshold in Da above which the mass of neutron should be added in
     894    // exact mass search
     895    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_EXACT_MASS, obj.getExactMass()));
     896    // Setting id
     897    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SETTING_ID, obj.getSettingId()));
     898    // E-value threshold to iteratively search a spectrum again, 0 = always
     899    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_RESEARCH_THRESH,  obj.getResearchThresh()));
     900    // E-value threshold to include a sequence in the iterative search, 0 =
     901    // all
     902    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SUBSET_THRESH,  obj.getSubsetThresh()));
     903    // E-value threshold to replace a hit, 0 = only if better
     904    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_REPLACE_THRESH, obj.getReplaceThresh()));
     905    // Eliminate charge reduced precursors in spectra (0=no, 1=yes)
     906    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_CULL, obj.getPrecursorCull()));
     907    // Turn off correlation correction to score (1=off, 0=use correlation)
     908    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_NO_CORRELATION_SCORE, obj.getNoCorrelationScore()));
     909    // Probability of consecutive ion (used in correlation correction)
     910    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PROB_FOLLOWING_ION, obj.getProbFollowingIon()));
     911    // N-term methionine should be cleaved
     912    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_NMETHIONINE_ATTRIBUTE,  obj.getNMethionineAttribute()));
     913    // Automatic mass tolerance adjustment fraction
     914    fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_AUTO_MASS_ADJUST, obj.getAutoMassAdjust()));
     915  for(TextField field : fields)
     916  {
     917   field.setHidden(true);
     918   field.setDisabled(true);
     919   fs.add(field);
     920  }
     921
     922    form.addFieldset(fs);
     923    return form;
     924  }
     925
    759926 
    760927  /**
  • trunk/client/servlet/src/org/proteios/gui/form/FormFactory.java

    r3865 r3866  
    22882288
    22892289 //Cleaning up from here
    2290 
    2291 
    2292   /**
    2293    * Form for new OMSSAParameterSetStorage item. The difference between
    2294    * calling getNewOMSSAParameterSetStorageForm(omssaParameterSetStorage) and
    2295    * getForm(OMSSAParameterSetStorage.class, omssaParameterSetStorage) when
    2296    * omssaParameterSetStorage != null, is that
    2297    * getForm(OMSSAParameterSetStorage.class, omssaParameterSetStorage) assumes
    2298    * that the omssaParameterSetStorage argument is stored in the database,
    2299    * i.e. that omssaParameterSetStorage.getId() is a valid item id, that can
    2300    * be used as value for a newIdField(), without an exception being thrown.
    2301    * Method getNewOMSSAParameterSetStorageForm() on the other hand only uses
    2302    * the omssaParameterSetStorage argument as a convenient place holder for
    2303    * default values for the OMSSAParameterSetStorage form fields.
    2304    *
    2305    * @param omssaParameterSetStorage OMSSAParameterSetStorage object (need not
    2306    *        be stored in database) with default field values.
    2307    * @return Form A form for setting OMSSAParameterSetStorage values.
    2308    */
    2309 
    2310 
    2311 
    2312   /**
    2313    * Form for saving an OMSSAParameterSetStorage item under a new name. This
    2314    * method only uses the omssaParameterSet argument as a convenient place
    2315    * holder for default values for the OMSSAParameterSet form fields.
    2316    *
    2317    * @param omssaParameterSetStorage OMSSAParameterSetStorage object with
    2318    *        default field values for name and parameter template file.
    2319    * @param omssaParameterSet OMSSAParameterSet object (need not be stored in
    2320    *        database) with default field values.
    2321    * @return Form A form for setting OMSSAParameterSetStorage values.
    2322    */
    2323   public Form getSaveAsOMSSAParameterSetStorageForm(
    2324       OMSSAParameterSetStorage omssaParameterSetStorage,
    2325       OMSSAParameterSet obj)
    2326   {
    2327     Form form = new Form("SaveAsOMSSAParameterSetStorage");
    2328     form.setTitle("SaveAsOMSSAParameterSetStorage");
    2329     Fieldset fs = new Fieldset("SaveAsOMSSAParameterSetStorage");
    2330     // OMSSAParameterSetStorage Name
    2331     TextField<String> nameF = new NameField();
    2332     fs.add(nameF);
    2333     nameF.setValue("OMSSA parameter set storage");
    2334 
    2335     // OMSSAParameterSetStorage Description
    2336     TextArea descF = new DescriptionField();
    2337     fs.add(descF);
    2338     descF.setValue("OMSSA parameter set storage");
    2339 
    2340     // OMSSA Parameters Template File
    2341     TextField<String> parameterFileF = new FileNameField();
    2342     fs.add(parameterFileF);
    2343     parameterFileF.setLabel("OMSSAParameterTemplateFile");
    2344     parameterFileF.setValue(getLocale().get("NotSpecifiedDefaultUsed"));
    2345     parameterFileF.setDisabled(true);
    2346 
    2347     // OMSSA Parameters Template File id
    2348     TextField<Integer> parameterFileIdF = new TextField<Integer>(AddOMSSAParameterSetStorage.VOMSSAPARAMETERTEMPLATEFILEID);
    2349     fs.add(parameterFileIdF);
    2350     parameterFileIdF.setHidden(true);
    2351     parameterFileIdF.setLabel("OMSSAParameterTemplateFileId");
    2352     parameterFileIdF.setValue(0);
    2353 
    2354     // Hidden text field for initial omssaParameterSetStorage id
    2355     TextField<Integer> iniOMSSApssIdF = new TextField<Integer>(
    2356       ViewActiveOMSSAParameterSetStorage.VOMSSAPARAMETERSETSTORAGEID);
    2357     iniOMSSApssIdF.setHidden(true);
    2358     if (omssaParameterSetStorage != null)
    2359     {
    2360       nameF.setValue(omssaParameterSetStorage.getName());
    2361       descF.setValue(omssaParameterSetStorage.getDescription());
    2362       iniOMSSApssIdF.setValue(omssaParameterSetStorage.getId());
    2363     if (omssaParameterSetStorage.getParameterFile() != null)
    2364       {
    2365         parameterFileIdF.setValue(omssaParameterSetStorage.getParameterFile().getId());
    2366         parameterFileF.setValue(omssaParameterSetStorage.getParameterFile().getPath().toString());
    2367       }
    2368     }
    2369     fs.add(iniOMSSApssIdF);
    2370     // Hidden text fields for transferring values of OMSSA parameter set
    2371   List<TextField> fields = new ArrayList<TextField>(51);
    2372     // Species (taxon)
    2373     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SPECIES, obj.getSpecies()));
    2374     // Search spectrum type
    2375     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_SPECTRUM_TYPE, obj.getSearchSpectrumType()));
    2376     // Precursor ion search type
    2377     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_SEARCH_TYPE,  obj.getPrecursorSearchType()));
    2378     // Product ion search type
    2379     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRODUCT_SEARCH_TYPE,  obj.getProductSearchType()));
    2380     // Ions to search 1
    2381     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_1, obj.getIonsToSearch1()));
    2382     // Ions to search 2
    2383     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_2, obj.getIonsToSearch2()));
    2384     // Precursor mass tolerance (Da)
    2385     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PEP_TOL, obj.getPepTol()));
    2386     // Product mass tolerance (Da)
    2387     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MSMS_TOL, obj.getMsMsTol()));
    2388     // Charge dependency of precursor mass tolerance (0 = none, 1 = linear)
    2389     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_ZDEP, obj.getZDep()));
    2390     // E-value cutoff
    2391     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTOFF, obj.getCutoff()));
    2392     // Peak low intensity cutoff (fraction of most intense)
    2393     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTLO, obj.getCutLo()));
    2394     // Peak high intensity cutoff (fraction of most intense)
    2395     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTHI, obj.getCutHi()));
    2396     // Peak intensity cutoff increment (fraction of most intense)
    2397     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTINC, obj.getCutInc()));
    2398     // Single charge window in Da
    2399     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_WIN, obj.getSingleWin()));
    2400     // Double charge window in Da
    2401     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_WIN, obj.getDoubleWin()));
    2402     // Number of peaks allowed in single charge window
    2403     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_NUM, obj.getSingleNum()));
    2404     // Number of peaks allowed in double charge window
    2405     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_NUM, obj.getDoubleNum()));
    2406     // Fixed modifications
    2407     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_FIXED, obj.getFixed()));
    2408     // Variable modifications
    2409     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_VARIABLE, obj.getVariable()));
    2410     // Enzyme
    2411     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_ENZYME, obj.getEnzyme()));
    2412     // Maximum missed cleavages
    2413     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MISSED_CLEAVE,  obj.getMissedCleave()));
    2414     // Hit list max length
    2415     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_HIT_LIST_LEN, obj.getHitListLen()));
    2416     // Sequence library
    2417     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DB, obj.getDb()));
    2418     // Number of top intensity peaks in first pass
    2419     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_TOP_HIT_NUM, obj.getTopHitNum()));
    2420     // Minimum number of m/z matches a sequence library peptide must have
    2421     // for the hit to the peptide to be recorded
    2422     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_HIT, obj.getMinHit()));
    2423     // Minimum number of m/z values a spectrum must have to be searched
    2424     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_SPECTRA, obj.getMinSpectra()));
    2425     // Scale
    2426     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SCALE, obj.getScale()));
    2427     // Maximum variable mod combinations searched per peptide
    2428     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_MODS, obj.getMaxMods()));
    2429     // Should charge plus one be determined algorithmically? (1=yes)
    2430     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_PLUS_ONE, obj.getMsCalcPlusOne()));
    2431     // How should precursor charges be determined? (1=believe the input
    2432     // file, 2=use a range)
    2433     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_CHARGE, obj.getMsCalcCharge()));
    2434     // Minimum precursor charge to search when not 1+
    2435     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_CHARGE, obj.getMinCharge()));
    2436     // Maximum precursor charge to search when not 1+
    2437     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_CHARGE, obj.getMaxCharge()));
    2438     // Minimum charge to start using multiply charged products
    2439     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CONSIDER_MULT,  obj.getConsiderMult()));
    2440     // Fraction of product peaks below precursor to determine +1 precursor
    2441     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PLUS_ONE, obj.getPlusOne()));
    2442     // Maximum product charge to search
    2443     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCT_CHARGE, obj.getMaxProductCharge()));
    2444     // Minimum number of precursors that match a spectrum
    2445     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PSEUDO_COUNT, obj.getPseudoCount()));
    2446     // Should first forward (b1) product ions be in search (1=no)
    2447     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_B1, obj.getSearchB1()));
    2448     // Should C terminus ions be searched (1=no)
    2449     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_C_TERM_PRODUCT,  obj.getSearchCTermProduct()));
    2450     // Max number of ions in each series being searched (0=all)
    2451     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCTIONS,  obj.getMaxProductions()));
    2452     // Minimum size of peptides for no-enzyme and semi-tryptic searches
    2453     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_NO_ENZYME,  obj.getMinNoEnzyme()));
    2454     // Maximum size of peptides for no-enzyme and semi-tryptic searches
    2455     // (0=none)
    2456     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_NO_ENZYME,  obj.getMaxNoEnzyme()));
    2457     // Threshold in Da above which the mass of neutron should be added in
    2458     // exact mass search
    2459     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_EXACT_MASS, obj.getExactMass()));
    2460     // Setting id
    2461     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SETTING_ID, obj.getSettingId()));
    2462     // E-value threshold to iteratively search a spectrum again, 0 = always
    2463     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_RESEARCH_THRESH,  obj.getResearchThresh()));
    2464     // E-value threshold to include a sequence in the iterative search, 0 =
    2465     // all
    2466     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SUBSET_THRESH,  obj.getSubsetThresh()));
    2467     // E-value threshold to replace a hit, 0 = only if better
    2468     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_REPLACE_THRESH, obj.getReplaceThresh()));
    2469     // Eliminate charge reduced precursors in spectra (0=no, 1=yes)
    2470     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_CULL, obj.getPrecursorCull()));
    2471     // Turn off correlation correction to score (1=off, 0=use correlation)
    2472     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_NO_CORRELATION_SCORE, obj.getNoCorrelationScore()));
    2473     // Probability of consecutive ion (used in correlation correction)
    2474     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PROB_FOLLOWING_ION, obj.getProbFollowingIon()));
    2475     // N-term methionine should be cleaved
    2476     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_NMETHIONINE_ATTRIBUTE,  obj.getNMethionineAttribute()));
    2477     // Automatic mass tolerance adjustment fraction
    2478     fields.add( new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_AUTO_MASS_ADJUST, obj.getAutoMassAdjust()));
    2479   for(TextField field : fields)
    2480   {
    2481    field.setHidden(true);
    2482    field.setDisabled(true);
    2483    fs.add(field);
    2484   }
    2485 
    2486     form.addFieldset(fs);
    2487     return form;
    2488   }
    2489 
    24902290
    24912291  public Form getOMSSAParameterSetForm(OMSSAParameterSet omssaParameterSet,
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