Changeset 3867


Ignore:
Timestamp:
Sep 23, 2010, 8:44:23 AM (13 years ago)
Author:
Gregory Vincic
Message:

Refs #698. Removed method getOMSSAParameterSetStorageForm 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/ViewActiveOMSSAParameterSetStorage.java

    r3825 r3867  
    11/*
    2  $Id$
    3 
    4  Copyright (C) 2006 Fredrik Levander, Gregory Vincic, Olle Mansson
    5  Copyright (C) 2007 Fredrik Levander, Gregory Vincic
    6 
    7  Files are copyright by their respective authors. The contributions to
    8  files where copyright is not explicitly stated can be traced with the
    9  source code revision system.
    10 
    11  This file is part of Proteios.
    12  Available at http://www.proteios.org/
    13 
    14  Proteios-2.x is free software; you can redistribute it and/or
    15  modify it under the terms of the GNU General Public License
    16  as published by the Free Software Foundation; either version 2
    17  of the License, or (at your option) any later version.
    18 
    19  Proteios is distributed in the hope that it will be useful,
    20  but WITHOUT ANY WARRANTY; without even the implied warranty of
    21  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    22  GNU General Public License for more details.
    23 
    24  You should have received a copy of the GNU General Public License
    25  along with this program; if not, write to the Free Software
    26  Foundation, Inc., 59 Temple Place - Suite 330,
    27  Boston, MA  02111-1307, USA.
    28  */
     2  $Id$
     3 
     4  Copyright (C) 2006 Fredrik Levander, Gregory Vincic, Olle Mansson
     5  Copyright (C) 2007 Fredrik Levander, Gregory Vincic
     6  Copyright (C) 2010 Gregory Vincic
     7 
     8  Files are copyright by their respective authors. The contributions to
     9  files where copyright is not explicitly stated can be traced with the
     10  source code revision system.
     11 
     12  This file is part of Proteios.
     13  Available at http://www.proteios.org/
     14 
     15  Proteios-2.x is free software; you can redistribute it and/or
     16  modify it under the terms of the GNU General Public License
     17  as published by the Free Software Foundation; either version 2
     18  of the License, or (at your option) any later version.
     19 
     20  Proteios is distributed in the hope that it will be useful,
     21  but WITHOUT ANY WARRANTY; without even the implied warranty of
     22  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     23  GNU General Public License for more details.
     24 
     25  You should have received a copy of the GNU General Public License
     26  along with this program; if not, write to the Free Software
     27  Foundation, Inc., 59 Temple Place - Suite 330,
     28  Boston, MA  02111-1307, USA.
     29*/
    2930package org.proteios.action.omssa;
    3031
    3132import java.io.InputStream;
    3233import java.util.ArrayList;
     34import java.util.HashMap;
     35import java.util.Hashtable;
    3336import java.util.List;
     37import java.util.Map;
    3438import org.proteios.ActionLink;
    3539import org.proteios.action.ProteiosAction;
    … …  
    4751import se.lu.thep.waf.constraints.InvalidParameterValue;
    4852import se.lu.thep.waf.constraints.VInteger;
     53import se.lu.thep.waf.constraints.VString;
    4954
    5055/**
    51  * @author olle
    52  */
     56  * @author olle
     57*/
    5358public class ViewActiveOMSSAParameterSetStorage
    54     extends ProteiosAction<ViewActiveOMSSAParameterSetStorage>
     59extends ProteiosAction<ViewActiveOMSSAParameterSetStorage>
    5560{
    56   public static final VInteger VOMSSAPARAMETERSETSTORAGEID = new VInteger(
    57     "active.omssaparametersetstorage.id", 1, false);
    58 
    59 
    60   @Override
    61   public void runMe()
    62       throws ActionException, InvalidParameterValue
    63   {
    64     /***********************************************************************
    65      * Properties
    66      */
    67     // Get the OMSSAParameterSetStorage item to use for the search
    68     Integer omssapssId = getValidInteger(VOMSSAPARAMETERSETSTORAGEID);
    69     log.debug("omssaParameterSetStorageId from VOMSSAPARAMETERSETSTORAGEID = " + omssapssId);
    70     // Get the OMSSAParameterSetStorage item to use for the search
    71     Boolean useWebInterfaceFlag = getValidBoolean(SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG);
    72     log.debug("useWebInterfaceFlag from SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG = " + useWebInterfaceFlag);
    73     if (useWebInterfaceFlag == null)
    74     {
    75       useWebInterfaceFlag = false;
    76     }
    77     log.debug("useWebInterfaceFlag = " + useWebInterfaceFlag);
    78     // SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG
    79     // Make sure an OMSSA parameter set has been selected
    80     if (omssapssId == null || omssapssId == 0)
    81     {
    82       List<Integer> omssapssIds = getValidIntegerList(FormFactory.VID);
    83       log.debug("omssapssIds from FormFactory.VID = " + omssapssIds);
    84       // Make sure at least one file has been selected
    85       if (omssapssIds == null || omssapssIds.size() == 0)
    86       {
    87         setError("Please select an OMSSA parameter set");
    88         return;
    89       }
    90       // Use first file in list
    91       omssapssId = omssapssIds.get(0);
    92     }
    93     log.debug("omssapssId = " + omssapssId);
    94     // Get the spectrum file items to use for the search
    95     List<Integer> spectrumFileIds = getValidIntegerList(SearchOMSSA.VSPECTRUMFILEID);
    96     log.debug("spectrumFileIds = " + spectrumFileIds);
    97     //
    98     DbControl dc = newDbControl();
    99     ItemFactory factory = getItemFactory(dc);
    100     OMSSAParameterSetStorage omssapss = factory.getById(OMSSAParameterSetStorage.class, omssapssId);
    101     // Get OMSSA parameter data from xml file
    102     OMSSAParameterFileUtil omssaParameterFileUtil = new OMSSAParameterFileUtil();
    103     InputStream iStream = omssapss.getParameterFile().getDownloadStream(0);
    104     omssaParameterFileUtil.setXMLInputStream(iStream);
    105     OMSSAParameterSet omssaParameterSet = omssaParameterFileUtil.fetchOMSSAParameterSet();
    106     // Get OMSSA parameter set option alternatives
    107     // Get OMSSAParameterSetOptionsUtil instance
    108     OMSSAParameterSetOptionsUtil omssaParameterSetOptionUtil = new OMSSAParameterSetOptionsUtil();
    109     omssaParameterSetOptionUtil.setWebInterfaceUsed(useWebInterfaceFlag);
    110     // Get enzyme option data
    111     List<String> enzymeStringList = omssaParameterSetOptionUtil.fetchEnzymeStringList();
    112     List<Option> enzymeOptionList = stringListToOptionList(enzymeStringList);
    113     // Get sequence library option data
    114     List<String> sequenceLibraryStringList = omssaParameterSetOptionUtil.fetchSequenceLibraryStringList();
    115     List<Option> sequenceLibraryOptionList = stringListToOptionList(sequenceLibraryStringList);
    116     // Get species option data
    117     List<String> speciesStringList = omssaParameterSetOptionUtil.fetchSpeciesStringList();
    118     List<Option> speciesOptionList = stringListToOptionList(speciesStringList);
    119     // Get fixed modifications option data
    120     List<String> fixedModsStringList = omssaParameterSetOptionUtil.fetchModificationStringList();
    121     List<Option> fixedModsOptionList = stringListToOptionList(fixedModsStringList);
    122     // Get variable modifications option data
    123     List<String> variableModsStringList = omssaParameterSetOptionUtil.fetchModificationStringList();
    124     List<Option> variableModsOptionList = stringListToOptionList(variableModsStringList);
    125     // OMSSA parameter set form
    126     Form omssaParameterSetForm = getFormFactory().getOMSSAParameterSetForm(omssaParameterSet,
    127       enzymeOptionList,
    128       sequenceLibraryOptionList,
    129       speciesOptionList,
    130       fixedModsOptionList,
    131       variableModsOptionList);
    132     /***********************************************************************
    133      * Annotations table
    134      */
    135     /*
    136     Annotator anna = new Annotator(getItemFactory(dc));
    137     TableFactory tableFactory = getTableFactory();
    138     tableFactory.reset();
    139     tableFactory.setItemClass(Annotation.class);
    140     ItemQuery<Annotation> annotationQuery = anna.getAnnotationSet(omssapss)
    141       .getAnnotations();
    142     tableFactory.setQuery(annotationQuery);
    143     tableFactory.setMaxResults(100);
    144     Table annotationsTable = tableFactory.build();
    145     */
    146     /***********************************************************************
    147      * Toolbar
    148      */
    149     Toolbar toolbar = new Toolbar();
    150     if (spectrumFileIds == null)
    151     {
    152       // Save OMSSA parameter set button
    153       ActionLink save = getActionLink(SaveOMSSAParameterSetStorage.class, "Save");
    154       save.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
    155       save.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, true);
    156       save.addParameter(ForwardField.VPARAM, ViewActiveOMSSAParameterSetStorage.class.getName());
    157       toolbar.add(save);
    158       // "Save As" OMSSA parameter set button
    159       ActionLink saveAs = getActionLink(SaveOMSSAParameterSetStorage.class, "SaveAs");
    160       saveAs.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
    161       saveAs.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, false);
    162       saveAs.addParameter(SearchOMSSA.VSAVEASOMSSAPARAMETERSETFLAG, true);
    163       saveAs.addParameter(ForwardField.VPARAM, ListOMSSAParameterSetStorage.class.getName());
    164       toolbar.add(saveAs);
    165     }
    166     else
    167     {
    168       // Save and Search OMSSA
    169       ActionLink searchOMSSA = getActionLink(SaveOMSSAParameterSetStorage.class, "SaveAndSearchOMSSA");
    170       searchOMSSA.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
    171       searchOMSSA.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, true);
    172       searchOMSSA.addParameter(ForwardField.VPARAM, SearchOMSSA.class.getName());
    173       for (Integer spectrumFileId : spectrumFileIds)
    174       {
    175         searchOMSSA.addParameter(SearchOMSSA.VSPECTRUMFILEID, spectrumFileId);
    176       }
    177       searchOMSSA.addParameter(SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG, useWebInterfaceFlag);
    178       toolbar.add(searchOMSSA);
    179       // "Save As" and Search OMSSA
    180       ActionLink saveAsAndSearchOMSSA = getActionLink(SaveOMSSAParameterSetStorage.class, "SaveAsAndSearchOMSSA");
    181       saveAsAndSearchOMSSA.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
    182       saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, false);
    183       saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VSAVEASOMSSAPARAMETERSETFLAG, true);
    184       saveAsAndSearchOMSSA.addParameter(ForwardField.VPARAM, SearchOMSSA.class.getName());
    185       for (Integer spectrumFileId : spectrumFileIds)
    186       {
    187         saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VSPECTRUMFILEID, spectrumFileId);
    188       }
    189       saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG, useWebInterfaceFlag);
    190       toolbar.add(saveAsAndSearchOMSSA);
    191     }
    192     omssaParameterSetForm.setToolbar(toolbar);
    193     /***********************************************************************
    194      * Layout
    195      */
    196     RowLayout layout = getLayoutFactory().getRowLayout();
    197     Title title = new Title("OMSSAParameterSet");
    198     title.setSubtitle(omssapss.getName());
    199     layout.add(title);
    200     //
    201     /*
    202     Tab annotations = new Tab("OtherSettings", "annotationsTab");
    203     annotations.setGuiElement(annotationsTable);
    204     ts.add(annotations);
    205     */
    206     layout.add(omssaParameterSetForm);
    207     setLayout(layout);
    208   }
    209 
    210 
    211   /**
    212    * Converts a list of alternating key and value strings
    213    * into a list of options.
    214    *
    215    * @param stringList List<String> A list of alternating key and value strings.
    216    * @return List<Option> A list of options
    217    */
    218   private List<Option> stringListToOptionList(List<String> stringList)
    219   {
    220     if (stringList == null)
    221     {
    222       return null;
    223     }
    224     List<Option> optionList = new ArrayList<Option>(0);
    225     for (int i = 0; i < stringList.size(); i = i + 2)
    226     {
    227       String key = stringList.get(i);
    228       String value = stringList.get(i + 1);
    229       /*
    230        * Note that the option "value" corresponds
    231        * to the "key" in the key-value string pair,
    232        * while the option "content" corresponds
    233        * to the "value" in the key-value string pair.
    234        */
    235       Option option = new Option(key, value);
    236       optionList.add(option);
    237     }
    238     return optionList;
    239   }
     61  public static final VInteger VOMSSAPARAMETERSETSTORAGEID = new VInteger(
     62  "active.omssaparametersetstorage.id", 1, false);
     63 
     64  @Override
     65  public void runMe()
     66  throws ActionException, InvalidParameterValue
     67  {
     68    // Get the OMSSAParameterSetStorage item to use for the search
     69    Integer omssapssId = getValidInteger(VOMSSAPARAMETERSETSTORAGEID);
     70    log.debug("omssaParameterSetStorageId from VOMSSAPARAMETERSETSTORAGEID = " + omssapssId);
     71    // Get the OMSSAParameterSetStorage item to use for the search
     72    Boolean useWebInterfaceFlag = getValidBoolean(SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG);
     73    log.debug("useWebInterfaceFlag from SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG = " + useWebInterfaceFlag);
     74    if (useWebInterfaceFlag == null)
     75    {
     76      useWebInterfaceFlag = false;
     77    }
     78    log.debug("useWebInterfaceFlag = " + useWebInterfaceFlag);
     79    // SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG
     80    // Make sure an OMSSA parameter set has been selected
     81    if (omssapssId == null || omssapssId == 0)
     82    {
     83      List<Integer> omssapssIds = getValidIntegerList(FormFactory.VID);
     84      log.debug("omssapssIds from FormFactory.VID = " + omssapssIds);
     85      // Make sure at least one file has been selected
     86      if (omssapssIds == null || omssapssIds.size() == 0)
     87      {
     88        setError("Please select an OMSSA parameter set");
     89        return;
     90      }
     91      // Use first file in list
     92      omssapssId = omssapssIds.get(0);
     93    }
     94    log.debug("omssapssId = " + omssapssId);
     95    // Get the spectrum file items to use for the search
     96    List<Integer> spectrumFileIds = getValidIntegerList(SearchOMSSA.VSPECTRUMFILEID);
     97    log.debug("spectrumFileIds = " + spectrumFileIds);
     98    //
     99    DbControl dc = newDbControl();
     100    ItemFactory factory = getItemFactory(dc);
     101    OMSSAParameterSetStorage omssapss = factory.getById(OMSSAParameterSetStorage.class, omssapssId);
     102    // Get OMSSA parameter data from xml file
     103    OMSSAParameterFileUtil omssaParameterFileUtil = new OMSSAParameterFileUtil();
     104    InputStream iStream = omssapss.getParameterFile().getDownloadStream(0);
     105    omssaParameterFileUtil.setXMLInputStream(iStream);
     106    OMSSAParameterSet omssaParameterSet = omssaParameterFileUtil.fetchOMSSAParameterSet();
     107    // Get OMSSA parameter set option alternatives
     108    // Get OMSSAParameterSetOptionsUtil instance
     109    OMSSAParameterSetOptionsUtil omssaParameterSetOptionUtil = new OMSSAParameterSetOptionsUtil();
     110    omssaParameterSetOptionUtil.setWebInterfaceUsed(useWebInterfaceFlag);
     111    // Get enzyme option data
     112    List<String> enzymeStringList = omssaParameterSetOptionUtil.fetchEnzymeStringList();
     113    List<Option> enzymeOptionList = stringListToOptionList(enzymeStringList);
     114    // Get sequence library option data
     115    List<String> sequenceLibraryStringList = omssaParameterSetOptionUtil.fetchSequenceLibraryStringList();
     116    List<Option> sequenceLibraryOptionList = stringListToOptionList(sequenceLibraryStringList);
     117    // Get species option data
     118    List<String> speciesStringList = omssaParameterSetOptionUtil.fetchSpeciesStringList();
     119    List<Option> speciesOptionList = stringListToOptionList(speciesStringList);
     120    // Get fixed modifications option data
     121    List<String> fixedModsStringList = omssaParameterSetOptionUtil.fetchModificationStringList();
     122    List<Option> fixedModsOptionList = stringListToOptionList(fixedModsStringList);
     123    // Get variable modifications option data
     124    List<String> variableModsStringList = omssaParameterSetOptionUtil.fetchModificationStringList();
     125    List<Option> variableModsOptionList = stringListToOptionList(variableModsStringList);
     126    // OMSSA parameter set form
     127    Form omssaParameterSetForm = getOMSSAParameterSetForm(omssaParameterSet,
     128    enzymeOptionList,
     129    sequenceLibraryOptionList,
     130    speciesOptionList,
     131    fixedModsOptionList,
     132    variableModsOptionList);
     133    /***********************************************************************
     134      * Toolbar
     135    */
     136    Toolbar toolbar = new Toolbar();
     137    if (spectrumFileIds == null)
     138    {
     139      // Save OMSSA parameter set button
     140      ActionLink save = getActionLink(SaveOMSSAParameterSetStorage.class, "Save");
     141      save.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
     142      save.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, true);
     143      save.addParameter(ForwardField.VPARAM, ViewActiveOMSSAParameterSetStorage.class.getName());
     144      toolbar.add(save);
     145      // "Save As" OMSSA parameter set button
     146      ActionLink saveAs = getActionLink(SaveOMSSAParameterSetStorage.class, "SaveAs");
     147      saveAs.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
     148      saveAs.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, false);
     149      saveAs.addParameter(SearchOMSSA.VSAVEASOMSSAPARAMETERSETFLAG, true);
     150      saveAs.addParameter(ForwardField.VPARAM, ListOMSSAParameterSetStorage.class.getName());
     151      toolbar.add(saveAs);
     152    }
     153    else
     154    {
     155      // Save and Search OMSSA
     156      ActionLink searchOMSSA = getActionLink(SaveOMSSAParameterSetStorage.class, "SaveAndSearchOMSSA");
     157      searchOMSSA.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
     158      searchOMSSA.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, true);
     159      searchOMSSA.addParameter(ForwardField.VPARAM, SearchOMSSA.class.getName());
     160      for (Integer spectrumFileId : spectrumFileIds)
     161      {
     162        searchOMSSA.addParameter(SearchOMSSA.VSPECTRUMFILEID, spectrumFileId);
     163      }
     164      searchOMSSA.addParameter(SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG, useWebInterfaceFlag);
     165      toolbar.add(searchOMSSA);
     166      // "Save As" and Search OMSSA
     167      ActionLink saveAsAndSearchOMSSA = getActionLink(SaveOMSSAParameterSetStorage.class, "SaveAsAndSearchOMSSA");
     168      saveAsAndSearchOMSSA.addParameter(VOMSSAPARAMETERSETSTORAGEID, omssapssId);
     169      saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VSAVEOMSSAPARAMETERSETFLAG, false);
     170      saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VSAVEASOMSSAPARAMETERSETFLAG, true);
     171      saveAsAndSearchOMSSA.addParameter(ForwardField.VPARAM, SearchOMSSA.class.getName());
     172      for (Integer spectrumFileId : spectrumFileIds)
     173      {
     174        saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VSPECTRUMFILEID, spectrumFileId);
     175      }
     176      saveAsAndSearchOMSSA.addParameter(SearchOMSSA.VOMSSAUSEWEBINTERFACEFLAG, useWebInterfaceFlag);
     177      toolbar.add(saveAsAndSearchOMSSA);
     178    }
     179    omssaParameterSetForm.setToolbar(toolbar);
     180    /***********************************************************************
     181      * Layout
     182    */
     183    RowLayout layout = getLayoutFactory().getRowLayout();
     184    Title title = new Title("OMSSAParameterSet");
     185    title.setSubtitle(omssapss.getName());
     186    layout.add(title);
     187    //
     188    layout.add(omssaParameterSetForm);
     189    setLayout(layout);
     190  }
     191 
     192  public Form getOMSSAParameterSetForm(OMSSAParameterSet omssaParameterSet,
     193  List<Option> enzymeOptionList,
     194  List<Option> sequenceLibraryOptionList,
     195  List<Option> speciesOptionList, List<Option> fixedModsOptionList,
     196  List<Option> variableModsOptionList)
     197  {
     198    OMSSAParameterFileUtil omssaParameterFileUtil = new OMSSAParameterFileUtil();
     199    // String delimRegex = new String(",\\ ");
     200    String delimRegex = new String(",");
     201    // Fetch help hash tables to find attribute strings
     202    Hashtable<String, String> searchTypeHT = omssaParameterFileUtil
     203    .fetchSearchTypeAttributeHashtable();
     204    Hashtable<String, String> ionTypeHT = omssaParameterFileUtil
     205    .fetchIonTypeAttributeHashtable();
     206    Hashtable<String, String> zDependenceHT = omssaParameterFileUtil
     207    .fetchZDependenceAttributeHashtable();
     208    Hashtable<String, String> enzymeHT = omssaParameterFileUtil
     209    .fetchEnzymeAttributeHashtable();
     210    Hashtable<String, String> speciesHT = omssaParameterFileUtil
     211    .fetchSpeciesAttributeHashtable();
     212    Hashtable<String, String> modificationHT = omssaParameterFileUtil
     213    .fetchModificationAttributeHashtable();
     214    // Fetch help lists to find menu alternatives
     215    List<String> searchTypeL = omssaParameterFileUtil
     216    .fetchSearchTypeAlternativesList();
     217    List<String> ionTypeL = omssaParameterFileUtil
     218    .fetchIonTypeAlternativesList();
     219    List<String> zDependenceL = omssaParameterFileUtil
     220    .fetchZDependenceAlternativesList();
     221    List<String> enzymeL = omssaParameterFileUtil
     222    .fetchEnzymeAlternativesList();
     223    List<String> speciesL = omssaParameterFileUtil
     224    .fetchSpeciesAlternativesList();
     225    List<String> modificationL = omssaParameterFileUtil
     226    .fetchModificationAlternativesList();
     227    // DbControl dc = project.getDbControl();
     228    Form form = new Form("OMSSAParameterSetForm");
     229    /*
     230      * String select box variables
     231    */
     232    VString validStringParam = null;
     233    List<String> stringList = null;
     234    List<Option> optionList = null;
     235    String selected = null;
     236    List<String> selectedList = null;
     237    /*
     238      * General field set
     239    */
     240    Fieldset generalFS = new Fieldset();
     241    generalFS.setTitle("OMSSAParameterSetGeneral");
     242    form.addFieldset(generalFS);
     243    // General, enzyme
     244    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_ENZYME;
     245    optionList = new ArrayList<Option>();
     246    for (String key : enzymeL)
     247    {
     248      optionList.add(new Option(key, enzymeHT.get(key)));
     249    }
     250    // Use input enzyme option list if present
     251    if (enzymeOptionList != null && enzymeOptionList.size() >= optionList
     252    .size())
     253    {
     254      optionList = enzymeOptionList;
     255    }
     256    selected = omssaParameterSet.getEnzyme();
     257    Select<VString> enzymeSelectBox = new Select<VString>(validStringParam,
     258    optionList);
     259    enzymeSelectBox.selectOption( selected);
     260    enzymeSelectBox.setLabel("OMSSAEnzymeSelect");
     261    generalFS.add(enzymeSelectBox);
     262    // General, maximum missed cleavages
     263    TextField<String> maxMissedCleavages = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MISSED_CLEAVE);
     264    maxMissedCleavages.setValue(omssaParameterSet.getMissedCleave());
     265    generalFS.add(maxMissedCleavages);
     266    // General, sequence library
     267    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_DB;
     268    optionList = new ArrayList<Option>();
     269    optionList.add(new Option("nr", "nr"));
     270    optionList.add(new Option("refseq_protein", "refseq_protein"));
     271    // Use input sequence library option list if present
     272    if (sequenceLibraryOptionList != null && sequenceLibraryOptionList
     273    .size() >= optionList.size())
     274    {
     275      optionList = sequenceLibraryOptionList;
     276    }
     277    selected = omssaParameterSet.getDb();
     278    Select<VString> sequenceLibrarySelectBox = new Select<VString>(
     279    validStringParam, optionList);
     280    sequenceLibrarySelectBox.selectOption( selected);
     281    sequenceLibrarySelectBox.setLabel("OMSSASequenceLibrarySelect");
     282    generalFS.add(sequenceLibrarySelectBox);
     283    // General, species
     284    /*
     285      * Species selection has one peculiarity: 1. It supports selection of
     286      * multiple items. The multiple selection items are stored in XML as a
     287      * string with items separated by ", ".
     288    */
     289    // Species
     290    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_SPECIES;
     291    optionList = new ArrayList<Option>();
     292    for (String key : speciesL)
     293    {
     294      optionList.add(new Option(key, speciesHT.get(key)));
     295    }
     296    // Use input species option list if present
     297    if (speciesOptionList != null && speciesOptionList.size() >= optionList.size())
     298    {
     299      optionList = speciesOptionList;
     300    }
     301    selected = omssaParameterSet.getSpecies();
     302    selectedList = listStringToStringList(selected, delimRegex);
     303    Select<VString> species = new Select<VString>(validStringParam,
     304    optionList, selectedList);
     305    species.setLabel("OMSSASpecies");
     306    species.setMultiple(true);
     307    species.setSize(7);
     308    generalFS.add(species);
     309    // General, hit list max length
     310    TextField<String> hitListMaxLength = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_HIT_LIST_LEN);
     311    hitListMaxLength.setValue(omssaParameterSet.getHitListLen());
     312    generalFS.add(hitListMaxLength);
     313    // General, e-value cutoff
     314    TextField<String> eValueCutoff = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTOFF);
     315    eValueCutoff.setValue(omssaParameterSet.getCutoff());
     316    generalFS.add(eValueCutoff);
     317    // General, fixed modifications
     318    /*
     319      * Fixed modifications selection has one peculiarity: 1. It supports
     320      * selection of multiple items. The multiple selection items are stored
     321      * in XML as a string with items separated by ", ".
     322    */
     323    // Fixed mods
     324    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_FIXED;
     325    optionList = new ArrayList<Option>();
     326    for (String key : modificationL)
     327    {
     328      optionList.add(new Option(key, modificationHT.get(key)));
     329    }
     330    // Use input fixed mods option list if present
     331    if (fixedModsOptionList != null && fixedModsOptionList.size() >= optionList
     332    .size())
     333    {
     334      optionList = fixedModsOptionList;
     335    }
     336    selected = omssaParameterSet.getFixed();
     337    selectedList = listStringToStringList(selected, delimRegex);
     338    Select<VString> fixedMods = new Select<VString>(validStringParam, optionList, selectedList);
     339    fixedMods.setLabel("OMSSAFixedMods");
     340    fixedMods.setMultiple(true);
     341    fixedMods.setSize(7);
     342    generalFS.add(fixedMods);
     343    // General, variable modifications
     344    /*
     345      * Variable modifications selection has one peculiarity: 1. It supports
     346      * selection of multiple items. The multiple selection items are stored
     347      * in XML as a string with items separated by ", ".
     348    */
     349    // Variable mods
     350    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_VARIABLE;
     351    optionList = new ArrayList<Option>();
     352    for (String key : modificationL)
     353    {
     354      optionList.add(new Option(key, modificationHT.get(key)));
     355    }
     356    // Use input variable mods option list if present
     357    if (variableModsOptionList != null && variableModsOptionList.size() >= optionList.size())
     358    {
     359      optionList = variableModsOptionList;
     360    }
     361    selected = omssaParameterSet.getVariable();
     362    selectedList = listStringToStringList(selected, delimRegex);
     363    Select<VString> variableMods = new Select<VString>(
     364    validStringParam, optionList, selectedList);
     365    variableMods.setLabel("OMSSAVariableMods");
     366    variableMods.setMultiple(true);
     367    variableMods.setSize(7);
     368    generalFS.add(variableMods);
     369    // General, maximum variable mod combinations searched per peptide
     370    TextField<String> maxMods = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_MODS);
     371    maxMods.setValue(omssaParameterSet.getMaxMods());
     372    generalFS.add(maxMods);
     373    // General, precursor mass tolerance (Da)
     374    TextField<String> precursorMassTolerance = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PEP_TOL);
     375    precursorMassTolerance.setValue(omssaParameterSet.getPepTol());
     376    generalFS.add(precursorMassTolerance);
     377    // General, product mass tolerance (Da)
     378    TextField<String> productMassTolerance = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MSMS_TOL);
     379    productMassTolerance.setValue(omssaParameterSet.getMsMsTol());
     380    generalFS.add(productMassTolerance);
     381    // General, precursor mass search type
     382    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_SEARCH_TYPE;
     383    optionList = new ArrayList<Option>();
     384    for (String key : searchTypeL)
     385    {
     386      optionList.add(new Option(key, searchTypeHT.get(key)));
     387    }
     388    selected = omssaParameterSet.getPrecursorSearchType();
     389    Select<VString> precursorMassSearchTypeSelectBox = new Select<VString>(
     390    validStringParam, optionList);
     391    precursorMassSearchTypeSelectBox.selectOption( selected);
     392    precursorMassSearchTypeSelectBox.setLabel("OMSSAPrecursorMassSearchTypeSelect");
     393    generalFS.add(precursorMassSearchTypeSelectBox);
     394    // General, product mass search type
     395    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_PRODUCT_SEARCH_TYPE;
     396    optionList = new ArrayList<Option>();
     397    for (String key : searchTypeL)
     398    {
     399      optionList.add(new Option(key, searchTypeHT.get(key)));
     400    }
     401    selected = omssaParameterSet.getProductSearchType();
     402    Select<VString> productMassSearchTypeSelectBox = new Select<VString>(
     403    validStringParam, optionList);
     404    productMassSearchTypeSelectBox.selectOption( selected);
     405    productMassSearchTypeSelectBox
     406    .setLabel("OMSSAProductMassSearchTypeSelect");
     407    generalFS.add(productMassSearchTypeSelectBox);
     408    // General, lower bound of precursor charge
     409    TextField<String> minPrecursorCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_CHARGE);
     410    minPrecursorCharge.setValue(omssaParameterSet.getMinCharge());
     411    generalFS.add(minPrecursorCharge);
     412    // General, upper bound of precursor charge
     413    TextField<String> maxPrecursorCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_CHARGE);
     414    maxPrecursorCharge.setValue(omssaParameterSet.getMaxCharge());
     415    generalFS.add(maxPrecursorCharge);
     416    // General, minimum charge to start using multiply charged products
     417    TextField<String> minChargeConsiderMult = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CONSIDER_MULT);
     418    minChargeConsiderMult.setValue(omssaParameterSet.getConsiderMult());
     419    generalFS.add(minChargeConsiderMult);
     420    // General, fraction of product peaks below precursor to determine +1
     421    // precursor
     422    TextField<String> fracProdPeaksPlusOne = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PLUS_ONE);
     423    fracProdPeaksPlusOne.setValue(omssaParameterSet.getPlusOne());
     424    generalFS.add(fracProdPeaksPlusOne);
     425    // General, peak low intensity cutoff (fraction of most intense)
     426    TextField<String> peakLowIntensityCutoff = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTLO);
     427    peakLowIntensityCutoff.setValue(omssaParameterSet.getCutLo());
     428    generalFS.add(peakLowIntensityCutoff);
     429    // General, number of top intensity peaks in first pass
     430    TextField<String> numTopIntensityPeaks = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_TOP_HIT_NUM);
     431    numTopIntensityPeaks.setValue(omssaParameterSet.getTopHitNum());
     432    generalFS.add(numTopIntensityPeaks);
     433    // General, ions to search 1
     434    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_1;
     435    optionList = new ArrayList<Option>();
     436    for (String key : ionTypeL)
     437    {
     438      optionList.add(new Option(key, ionTypeHT.get(key)));
     439    }
     440    selected = omssaParameterSet.getIonsToSearch1();
     441    Select<VString> ionsToSearch1SelectBox = new Select<VString>(validStringParam, optionList);
     442    ionsToSearch1SelectBox.selectOption( selected);
     443    ionsToSearch1SelectBox.setLabel("OMSSAIonsToSearch1Select");
     444    generalFS.add(ionsToSearch1SelectBox);
     445    // General, ions to search 2
     446    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_2;
     447    optionList = new ArrayList<Option>();
     448    for (String key : ionTypeL)
     449    {
     450      optionList.add(new Option(key, ionTypeHT.get(key)));
     451    }
     452    selected = omssaParameterSet.getIonsToSearch2();
     453    Select<VString> ionsToSearch2SelectBox = new Select<VString>(validStringParam, optionList);
     454    ionsToSearch2SelectBox.selectOption( selected);
     455    ionsToSearch2SelectBox.setLabel("OMSSAIonsToSearch2Select");
     456    generalFS.add(ionsToSearch2SelectBox);
     457    /*
     458      * Extra field set
     459    */
     460    Fieldset extraFS = new Fieldset();
     461    extraFS.setTitle("OMSSAParameterSetExtra");
     462    form.addFieldset(extraFS);
     463    // Extra, z dependence
     464    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_ZDEP;
     465    optionList = new ArrayList<Option>();
     466    for (String key : zDependenceL)
     467    {
     468      optionList.add(new Option(key, zDependenceHT.get(key)));
     469    }
     470    selected = omssaParameterSet.getZDep();
     471    Select<VString> zDepSelectBox = new Select<VString>(validStringParam, optionList);
     472    zDepSelectBox.selectOption( selected);
     473    zDepSelectBox.setLabel("OMSSAZDepSelect");
     474    extraFS.add(zDepSelectBox);
     475    // Extra, peak high intensity cutoff (fraction of most intense)
     476    TextField<String> peakHighIntensityCutoff = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTHI);
     477    peakHighIntensityCutoff.setValue(omssaParameterSet.getCutHi());
     478    extraFS.add(peakHighIntensityCutoff);
     479    // Extra, peak intensity cutoff increment (fraction of most intense)
     480    TextField<String> peakIntensityCutInc = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTINC);
     481    peakIntensityCutInc.setValue(omssaParameterSet.getCutInc());
     482    extraFS.add(peakIntensityCutInc);
     483    // Extra, single win
     484    TextField<String> singleWin = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_WIN);
     485    singleWin.setValue(omssaParameterSet.getSingleWin());
     486    extraFS.add(singleWin);
     487    // Extra, double win
     488    TextField<String> doubleWin = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_WIN);
     489    doubleWin.setValue(omssaParameterSet.getDoubleWin());
     490    extraFS.add(doubleWin);
     491    // Extra, single num
     492    TextField<String> singleNum = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_NUM);
     493    singleNum.setValue(omssaParameterSet.getSingleNum());
     494    extraFS.add(singleNum);
     495    // Extra, double num
     496    TextField<String> doubleNum = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_NUM);
     497    doubleNum.setValue(omssaParameterSet.getDoubleNum());
     498    extraFS.add(doubleNum);
     499    // Extra, min hit
     500    TextField<String> minHit = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_HIT);
     501    minHit.setValue(omssaParameterSet.getMinHit());
     502    extraFS.add(minHit);
     503    // Extra, min spectra
     504    TextField<String> minSpectra = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_SPECTRA);
     505    minSpectra.setValue(omssaParameterSet.getMinSpectra());
     506    extraFS.add(minSpectra);
     507    // Extra, scale
     508    TextField<String> scale = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SCALE);
     509    scale.setValue(omssaParameterSet.getScale());
     510    extraFS.add(scale);
     511    // Extra, ms calc plus one
     512    TextField<String> msCalcPlusOne = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_PLUS_ONE);
     513    msCalcPlusOne.setValue(omssaParameterSet.getMsCalcPlusOne());
     514    extraFS.add(msCalcPlusOne);
     515    // Extra, ms calc charge
     516    TextField<String> msCalcCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_CHARGE);
     517    msCalcCharge.setValue(omssaParameterSet.getMsCalcCharge());
     518    extraFS.add(msCalcCharge);
     519    // Extra, max product charge
     520    TextField<String> maxProductCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCT_CHARGE);
     521    maxProductCharge.setValue(omssaParameterSet.getMaxProductCharge());
     522    extraFS.add(maxProductCharge);
     523    // Extra, pseudo count
     524    TextField<String> pseudoCount = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PSEUDO_COUNT);
     525    pseudoCount.setValue(omssaParameterSet.getPseudoCount());
     526    extraFS.add(pseudoCount);
     527    // Extra, search b1
     528    TextField<String> searchB1 = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_B1);
     529    searchB1.setValue(omssaParameterSet.getSearchB1());
     530    extraFS.add(searchB1);
     531    // Extra, search C terminus product
     532    TextField<String> searchCTermProduct = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_C_TERM_PRODUCT);
     533    searchCTermProduct.setValue(omssaParameterSet.getSearchCTermProduct());
     534    extraFS.add(searchCTermProduct);
     535    // Extra, max productions
     536    TextField<String> maxProductions = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCTIONS);
     537    maxProductions.setValue(omssaParameterSet.getMaxProductions());
     538    extraFS.add(maxProductions);
     539    // Extra, min no enzyme
     540    TextField<String> minNoEnzyme = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_NO_ENZYME);
     541    minNoEnzyme.setValue(omssaParameterSet.getMinNoEnzyme());
     542    extraFS.add(minNoEnzyme);
     543    // Extra, max no enzyme
     544    TextField<String> maxNoEnzyme = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_NO_ENZYME);
     545    maxNoEnzyme.setValue(omssaParameterSet.getMaxNoEnzyme());
     546    extraFS.add(maxNoEnzyme);
     547    // Extra, exact mass
     548    TextField<String> exactMass = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_EXACT_MASS);
     549    exactMass.setValue(omssaParameterSet.getExactMass());
     550    extraFS.add(exactMass);
     551    // Extra, setting id
     552    TextField<String> settingId = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SETTING_ID);
     553    settingId.setValue(omssaParameterSet.getSettingId());
     554    extraFS.add(settingId);
     555    // Extra, research threshold
     556    TextField<String> researchThreshold = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_RESEARCH_THRESH);
     557    researchThreshold.setValue(omssaParameterSet.getResearchThresh());
     558    extraFS.add(researchThreshold);
     559    // Extra, subset threshold
     560    TextField<String> subsetThreshold = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SUBSET_THRESH);
     561    subsetThreshold.setValue(omssaParameterSet.getSubsetThresh());
     562    extraFS.add(subsetThreshold);
     563    // Extra, replace threshold
     564    TextField<String> replaceThreshold = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_REPLACE_THRESH);
     565    replaceThreshold.setValue(omssaParameterSet.getReplaceThresh());
     566    extraFS.add(replaceThreshold);
     567    // Extra, precursor cull
     568    TextField<String> precursorCull = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_CULL);
     569    precursorCull.setValue(omssaParameterSet.getPrecursorCull());
     570    extraFS.add(precursorCull);
     571    // Extra, no correlation score
     572    TextField<String> noCorrelationScore = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_NO_CORRELATION_SCORE);
     573    noCorrelationScore.setValue(omssaParameterSet.getNoCorrelationScore());
     574    extraFS.add(noCorrelationScore);
     575    // Extra, prob following ion
     576    TextField<String> probFollowingIon = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PROB_FOLLOWING_ION);
     577    probFollowingIon.setValue(omssaParameterSet.getProbFollowingIon());
     578    extraFS.add(probFollowingIon);
     579    // Extra, nMethionine
     580    validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_NMETHIONINE_ATTRIBUTE;
     581    optionList = new ArrayList<Option>();
     582    optionList.add(new Option("true", "true"));
     583    optionList.add(new Option("false", "false"));
     584    selected = omssaParameterSet.getNMethionineAttribute();
     585    Select<VString> nMethionineSelectBox = new Select<VString>(validStringParam, optionList);
     586    nMethionineSelectBox.selectOption( selected);
     587    nMethionineSelectBox.setLabel("OMSSANMethionineSelect");
     588    extraFS.add(nMethionineSelectBox);
     589    // Extra, auto mass adjust
     590    TextField<String> autoMassAdjust = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_AUTO_MASS_ADJUST);
     591    autoMassAdjust.setValue(omssaParameterSet.getAutoMassAdjust());
     592    extraFS.add(autoMassAdjust);
     593    //
     594    return form;
     595  }
     596 
     597  /**
     598    * Converts a list of alternating key and value strings
     599    * into a list of options.
     600    *
     601    * @param stringList List<String> A list of alternating key and value strings.
     602    * @return List<Option> A list of options
     603  */
     604  private List<Option> stringListToOptionList(List<String> stringList)
     605  {
     606    if (stringList == null)
     607    {
     608      return null;
     609    }
     610    List<Option> optionList = new ArrayList<Option>(0);
     611    for (int i = 0; i < stringList.size(); i = i + 2)
     612    {
     613      String key = stringList.get(i);
     614      String value = stringList.get(i + 1);
     615      /*
     616        * Note that the option "value" corresponds
     617        * to the "key" in the key-value string pair,
     618        * while the option "content" corresponds
     619        * to the "value" in the key-value string pair.
     620      */
     621      Option option = new Option(key, value);
     622      optionList.add(option);
     623    }
     624    return optionList;
     625  }
     626 
     627  /**
     628    * Converts a list String to a list with String elements. If the list string
     629    * contains two delimiter strings directly after each other, an empty string
     630    * element will be added to the list in the corresponding place. Example:
     631    * List string "one, two, three" will be converted to a list with the three
     632    * String elements "one", "two", and "three" using delimiter regular
     633    * expression ",\\ ".
     634    *
     635    * @param listString String A string with a list
     636    * @param delimiterRegex String A regular expression for the delimiter
     637    *        between list elements
     638    * @return List<String> A list of String elements
     639  */
     640  private List<String> listStringToStringList(String listString,
     641  String delimiterRegex)
     642  {
     643    List<String> stringList = null;
     644    if (listString != null)
     645    {
     646      stringList = new ArrayList<String>(0);
     647      for (String part : listString.split(delimiterRegex, -1))
     648      {
     649        // Add list part if not already in list
     650        if (part != null && !stringList.contains(part))
     651        {
     652          stringList.add(part);
     653        }
     654      }
     655    }
     656    return stringList;
     657  }
     658 
    240659}

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

    r3866 r3867  
    22882288
    22892289 //Cleaning up from here
    2290 
    2291   public Form getOMSSAParameterSetForm(OMSSAParameterSet omssaParameterSet,
    2292       List<Option> enzymeOptionList,
    2293       List<Option> sequenceLibraryOptionList,
    2294       List<Option> speciesOptionList, List<Option> fixedModsOptionList,
    2295       List<Option> variableModsOptionList)
    2296   {
    2297     OMSSAParameterFileUtil omssaParameterFileUtil = new OMSSAParameterFileUtil();
    2298     // String delimRegex = new String(",\\ ");
    2299     String delimRegex = new String(",");
    2300     // Fetch help hash tables to find attribute strings
    2301     Hashtable<String, String> searchTypeHT = omssaParameterFileUtil
    2302       .fetchSearchTypeAttributeHashtable();
    2303     Hashtable<String, String> ionTypeHT = omssaParameterFileUtil
    2304       .fetchIonTypeAttributeHashtable();
    2305     Hashtable<String, String> zDependenceHT = omssaParameterFileUtil
    2306       .fetchZDependenceAttributeHashtable();
    2307     Hashtable<String, String> enzymeHT = omssaParameterFileUtil
    2308       .fetchEnzymeAttributeHashtable();
    2309     Hashtable<String, String> speciesHT = omssaParameterFileUtil
    2310       .fetchSpeciesAttributeHashtable();
    2311     Hashtable<String, String> modificationHT = omssaParameterFileUtil
    2312       .fetchModificationAttributeHashtable();
    2313     // Fetch help lists to find menu alternatives
    2314     List<String> searchTypeL = omssaParameterFileUtil
    2315       .fetchSearchTypeAlternativesList();
    2316     List<String> ionTypeL = omssaParameterFileUtil
    2317       .fetchIonTypeAlternativesList();
    2318     List<String> zDependenceL = omssaParameterFileUtil
    2319       .fetchZDependenceAlternativesList();
    2320     List<String> enzymeL = omssaParameterFileUtil
    2321       .fetchEnzymeAlternativesList();
    2322     List<String> speciesL = omssaParameterFileUtil
    2323       .fetchSpeciesAlternativesList();
    2324     List<String> modificationL = omssaParameterFileUtil
    2325       .fetchModificationAlternativesList();
    2326     // DbControl dc = project.getDbControl();
    2327     Form form = new Form("OMSSAParameterSetForm");
    2328     /*
    2329      * String select box variables
    2330      */
    2331     VString validStringParam = null;
    2332     List<String> stringList = null;
    2333     List<Option> optionList = null;
    2334     String selected = null;
    2335     List<String> selectedList = null;
    2336     /*
    2337      * General field set
    2338      */
    2339     Fieldset generalFS = new Fieldset();
    2340     generalFS.setTitle("OMSSAParameterSetGeneral");
    2341     form.addFieldset(generalFS);
    2342     // General, enzyme
    2343     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_ENZYME;
    2344     optionList = new ArrayList<Option>();
    2345     for (String key : enzymeL)
    2346     {
    2347       optionList.add(new Option(key, enzymeHT.get(key)));
    2348     }
    2349     // Use input enzyme option list if present
    2350     if (enzymeOptionList != null && enzymeOptionList.size() >= optionList
    2351       .size())
    2352     {
    2353       optionList = enzymeOptionList;
    2354     }
    2355     selected = omssaParameterSet.getEnzyme();
    2356     Select<VString> enzymeSelectBox = new Select<VString>(validStringParam,
    2357       optionList);
    2358   enzymeSelectBox.selectOption( selected);
    2359     enzymeSelectBox.setLabel("OMSSAEnzymeSelect");
    2360     generalFS.add(enzymeSelectBox);
    2361     // General, maximum missed cleavages
    2362     TextField<String> maxMissedCleavages = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MISSED_CLEAVE);
    2363     maxMissedCleavages.setValue(omssaParameterSet.getMissedCleave());
    2364     generalFS.add(maxMissedCleavages);
    2365     // General, sequence library
    2366     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_DB;
    2367     optionList = new ArrayList<Option>();
    2368     optionList.add(new Option("nr", "nr"));
    2369     optionList.add(new Option("refseq_protein", "refseq_protein"));
    2370     // Use input sequence library option list if present
    2371     if (sequenceLibraryOptionList != null && sequenceLibraryOptionList
    2372       .size() >= optionList.size())
    2373     {
    2374       optionList = sequenceLibraryOptionList;
    2375     }
    2376     selected = omssaParameterSet.getDb();
    2377     Select<VString> sequenceLibrarySelectBox = new Select<VString>(
    2378       validStringParam, optionList);
    2379   sequenceLibrarySelectBox.selectOption( selected);
    2380     sequenceLibrarySelectBox.setLabel("OMSSASequenceLibrarySelect");
    2381     generalFS.add(sequenceLibrarySelectBox);
    2382     // General, species
    2383     /*
    2384      * Species selection has one peculiarity: 1. It supports selection of
    2385      * multiple items. The multiple selection items are stored in XML as a
    2386      * string with items separated by ", ".
    2387      */
    2388     // Species
    2389     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_SPECIES;
    2390     optionList = new ArrayList<Option>();
    2391     for (String key : speciesL)
    2392     {
    2393       optionList.add(new Option(key, speciesHT.get(key)));
    2394     }
    2395     // Use input species option list if present
    2396     if (speciesOptionList != null && speciesOptionList.size() >= optionList.size())
    2397     {
    2398       optionList = speciesOptionList;
    2399     }
    2400     selected = omssaParameterSet.getSpecies();
    2401     selectedList = listStringToStringList(selected, delimRegex);
    2402     Select<VString> species = new Select<VString>(validStringParam,
    2403       optionList, selectedList);
    2404     species.setLabel("OMSSASpecies");
    2405     species.setMultiple(true);
    2406     species.setSize(7);
    2407     generalFS.add(species);
    2408     // General, hit list max length
    2409     TextField<String> hitListMaxLength = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_HIT_LIST_LEN);
    2410     hitListMaxLength.setValue(omssaParameterSet.getHitListLen());
    2411     generalFS.add(hitListMaxLength);
    2412     // General, e-value cutoff
    2413     TextField<String> eValueCutoff = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTOFF);
    2414     eValueCutoff.setValue(omssaParameterSet.getCutoff());
    2415     generalFS.add(eValueCutoff);
    2416     // General, fixed modifications
    2417     /*
    2418      * Fixed modifications selection has one peculiarity: 1. It supports
    2419      * selection of multiple items. The multiple selection items are stored
    2420      * in XML as a string with items separated by ", ".
    2421      */
    2422     // Fixed mods
    2423     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_FIXED;
    2424     optionList = new ArrayList<Option>();
    2425     for (String key : modificationL)
    2426     {
    2427       optionList.add(new Option(key, modificationHT.get(key)));
    2428     }
    2429     // Use input fixed mods option list if present
    2430     if (fixedModsOptionList != null && fixedModsOptionList.size() >= optionList
    2431       .size())
    2432     {
    2433       optionList = fixedModsOptionList;
    2434     }
    2435     selected = omssaParameterSet.getFixed();
    2436     selectedList = listStringToStringList(selected, delimRegex);
    2437     Select<VString> fixedMods = new Select<VString>(validStringParam, optionList, selectedList);
    2438     fixedMods.setLabel("OMSSAFixedMods");
    2439     fixedMods.setMultiple(true);
    2440     fixedMods.setSize(7);
    2441     generalFS.add(fixedMods);
    2442     // General, variable modifications
    2443     /*
    2444      * Variable modifications selection has one peculiarity: 1. It supports
    2445      * selection of multiple items. The multiple selection items are stored
    2446      * in XML as a string with items separated by ", ".
    2447      */
    2448     // Variable mods
    2449     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_VARIABLE;
    2450     optionList = new ArrayList<Option>();
    2451     for (String key : modificationL)
    2452     {
    2453       optionList.add(new Option(key, modificationHT.get(key)));
    2454     }
    2455     // Use input variable mods option list if present
    2456     if (variableModsOptionList != null && variableModsOptionList.size() >= optionList.size())
    2457     {
    2458       optionList = variableModsOptionList;
    2459     }
    2460     selected = omssaParameterSet.getVariable();
    2461     selectedList = listStringToStringList(selected, delimRegex);
    2462     Select<VString> variableMods = new Select<VString>(
    2463       validStringParam, optionList, selectedList);
    2464     variableMods.setLabel("OMSSAVariableMods");
    2465     variableMods.setMultiple(true);
    2466     variableMods.setSize(7);
    2467     generalFS.add(variableMods);
    2468     // General, maximum variable mod combinations searched per peptide
    2469     TextField<String> maxMods = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_MODS);
    2470     maxMods.setValue(omssaParameterSet.getMaxMods());
    2471     generalFS.add(maxMods);
    2472     // General, precursor mass tolerance (Da)
    2473     TextField<String> precursorMassTolerance = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PEP_TOL);
    2474     precursorMassTolerance.setValue(omssaParameterSet.getPepTol());
    2475     generalFS.add(precursorMassTolerance);
    2476     // General, product mass tolerance (Da)
    2477     TextField<String> productMassTolerance = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MSMS_TOL);
    2478     productMassTolerance.setValue(omssaParameterSet.getMsMsTol());
    2479     generalFS.add(productMassTolerance);
    2480     // General, precursor mass search type
    2481     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_SEARCH_TYPE;
    2482     optionList = new ArrayList<Option>();
    2483     for (String key : searchTypeL)
    2484     {
    2485       optionList.add(new Option(key, searchTypeHT.get(key)));
    2486     }
    2487     selected = omssaParameterSet.getPrecursorSearchType();
    2488     Select<VString> precursorMassSearchTypeSelectBox = new Select<VString>(
    2489       validStringParam, optionList);
    2490   precursorMassSearchTypeSelectBox.selectOption( selected);
    2491     precursorMassSearchTypeSelectBox.setLabel("OMSSAPrecursorMassSearchTypeSelect");
    2492     generalFS.add(precursorMassSearchTypeSelectBox);
    2493     // General, product mass search type
    2494     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_PRODUCT_SEARCH_TYPE;
    2495     optionList = new ArrayList<Option>();
    2496     for (String key : searchTypeL)
    2497     {
    2498       optionList.add(new Option(key, searchTypeHT.get(key)));
    2499     }
    2500     selected = omssaParameterSet.getProductSearchType();
    2501     Select<VString> productMassSearchTypeSelectBox = new Select<VString>(
    2502       validStringParam, optionList);
    2503   productMassSearchTypeSelectBox.selectOption( selected);
    2504     productMassSearchTypeSelectBox
    2505       .setLabel("OMSSAProductMassSearchTypeSelect");
    2506     generalFS.add(productMassSearchTypeSelectBox);
    2507     // General, lower bound of precursor charge
    2508     TextField<String> minPrecursorCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_CHARGE);
    2509     minPrecursorCharge.setValue(omssaParameterSet.getMinCharge());
    2510     generalFS.add(minPrecursorCharge);
    2511     // General, upper bound of precursor charge
    2512     TextField<String> maxPrecursorCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_CHARGE);
    2513     maxPrecursorCharge.setValue(omssaParameterSet.getMaxCharge());
    2514     generalFS.add(maxPrecursorCharge);
    2515     // General, minimum charge to start using multiply charged products
    2516     TextField<String> minChargeConsiderMult = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CONSIDER_MULT);
    2517     minChargeConsiderMult.setValue(omssaParameterSet.getConsiderMult());
    2518     generalFS.add(minChargeConsiderMult);
    2519     // General, fraction of product peaks below precursor to determine +1
    2520     // precursor
    2521     TextField<String> fracProdPeaksPlusOne = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PLUS_ONE);
    2522     fracProdPeaksPlusOne.setValue(omssaParameterSet.getPlusOne());
    2523     generalFS.add(fracProdPeaksPlusOne);
    2524     // General, peak low intensity cutoff (fraction of most intense)
    2525     TextField<String> peakLowIntensityCutoff = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTLO);
    2526     peakLowIntensityCutoff.setValue(omssaParameterSet.getCutLo());
    2527     generalFS.add(peakLowIntensityCutoff);
    2528     // General, number of top intensity peaks in first pass
    2529     TextField<String> numTopIntensityPeaks = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_TOP_HIT_NUM);
    2530     numTopIntensityPeaks.setValue(omssaParameterSet.getTopHitNum());
    2531     generalFS.add(numTopIntensityPeaks);
    2532     // General, ions to search 1
    2533     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_1;
    2534     optionList = new ArrayList<Option>();
    2535     for (String key : ionTypeL)
    2536     {
    2537       optionList.add(new Option(key, ionTypeHT.get(key)));
    2538     }
    2539     selected = omssaParameterSet.getIonsToSearch1();
    2540     Select<VString> ionsToSearch1SelectBox = new Select<VString>(validStringParam, optionList);
    2541   ionsToSearch1SelectBox.selectOption( selected);
    2542     ionsToSearch1SelectBox.setLabel("OMSSAIonsToSearch1Select");
    2543     generalFS.add(ionsToSearch1SelectBox);
    2544     // General, ions to search 2
    2545     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_IONS_TO_SEARCH_2;
    2546     optionList = new ArrayList<Option>();
    2547     for (String key : ionTypeL)
    2548     {
    2549       optionList.add(new Option(key, ionTypeHT.get(key)));
    2550     }
    2551     selected = omssaParameterSet.getIonsToSearch2();
    2552     Select<VString> ionsToSearch2SelectBox = new Select<VString>(validStringParam, optionList);
    2553   ionsToSearch2SelectBox.selectOption( selected);
    2554     ionsToSearch2SelectBox.setLabel("OMSSAIonsToSearch2Select");
    2555     generalFS.add(ionsToSearch2SelectBox);
    2556     /*
    2557      * Extra field set
    2558      */
    2559     Fieldset extraFS = new Fieldset();
    2560     extraFS.setTitle("OMSSAParameterSetExtra");
    2561     form.addFieldset(extraFS);
    2562     // Extra, z dependence
    2563     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_ZDEP;
    2564     optionList = new ArrayList<Option>();
    2565     for (String key : zDependenceL)
    2566     {
    2567       optionList.add(new Option(key, zDependenceHT.get(key)));
    2568     }
    2569     selected = omssaParameterSet.getZDep();
    2570     Select<VString> zDepSelectBox = new Select<VString>(validStringParam, optionList);
    2571   zDepSelectBox.selectOption( selected);
    2572     zDepSelectBox.setLabel("OMSSAZDepSelect");
    2573     extraFS.add(zDepSelectBox);
    2574     // Extra, peak high intensity cutoff (fraction of most intense)
    2575     TextField<String> peakHighIntensityCutoff = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTHI);
    2576     peakHighIntensityCutoff.setValue(omssaParameterSet.getCutHi());
    2577     extraFS.add(peakHighIntensityCutoff);
    2578     // Extra, peak intensity cutoff increment (fraction of most intense)
    2579     TextField<String> peakIntensityCutInc = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_CUTINC);
    2580     peakIntensityCutInc.setValue(omssaParameterSet.getCutInc());
    2581     extraFS.add(peakIntensityCutInc);
    2582     // Extra, single win
    2583     TextField<String> singleWin = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_WIN);
    2584     singleWin.setValue(omssaParameterSet.getSingleWin());
    2585     extraFS.add(singleWin);
    2586     // Extra, double win
    2587     TextField<String> doubleWin = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_WIN);
    2588     doubleWin.setValue(omssaParameterSet.getDoubleWin());
    2589     extraFS.add(doubleWin);
    2590     // Extra, single num
    2591     TextField<String> singleNum = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SINGLE_NUM);
    2592     singleNum.setValue(omssaParameterSet.getSingleNum());
    2593     extraFS.add(singleNum);
    2594     // Extra, double num
    2595     TextField<String> doubleNum = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_DOUBLE_NUM);
    2596     doubleNum.setValue(omssaParameterSet.getDoubleNum());
    2597     extraFS.add(doubleNum);
    2598     // Extra, min hit
    2599     TextField<String> minHit = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_HIT);
    2600     minHit.setValue(omssaParameterSet.getMinHit());
    2601     extraFS.add(minHit);
    2602     // Extra, min spectra
    2603     TextField<String> minSpectra = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_SPECTRA);
    2604     minSpectra.setValue(omssaParameterSet.getMinSpectra());
    2605     extraFS.add(minSpectra);
    2606     // Extra, scale
    2607     TextField<String> scale = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SCALE);
    2608     scale.setValue(omssaParameterSet.getScale());
    2609     extraFS.add(scale);
    2610     // Extra, ms calc plus one
    2611     TextField<String> msCalcPlusOne = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_PLUS_ONE);
    2612     msCalcPlusOne.setValue(omssaParameterSet.getMsCalcPlusOne());
    2613     extraFS.add(msCalcPlusOne);
    2614     // Extra, ms calc charge
    2615     TextField<String> msCalcCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MS_CALC_CHARGE);
    2616     msCalcCharge.setValue(omssaParameterSet.getMsCalcCharge());
    2617     extraFS.add(msCalcCharge);
    2618     // Extra, max product charge
    2619     TextField<String> maxProductCharge = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCT_CHARGE);
    2620     maxProductCharge.setValue(omssaParameterSet.getMaxProductCharge());
    2621     extraFS.add(maxProductCharge);
    2622     // Extra, pseudo count
    2623     TextField<String> pseudoCount = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PSEUDO_COUNT);
    2624     pseudoCount.setValue(omssaParameterSet.getPseudoCount());
    2625     extraFS.add(pseudoCount);
    2626     // Extra, search b1
    2627     TextField<String> searchB1 = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_B1);
    2628     searchB1.setValue(omssaParameterSet.getSearchB1());
    2629     extraFS.add(searchB1);
    2630     // Extra, search C terminus product
    2631     TextField<String> searchCTermProduct = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SEARCH_C_TERM_PRODUCT);
    2632     searchCTermProduct.setValue(omssaParameterSet.getSearchCTermProduct());
    2633     extraFS.add(searchCTermProduct);
    2634     // Extra, max productions
    2635     TextField<String> maxProductions = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_PRODUCTIONS);
    2636     maxProductions.setValue(omssaParameterSet.getMaxProductions());
    2637     extraFS.add(maxProductions);
    2638     // Extra, min no enzyme
    2639     TextField<String> minNoEnzyme = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MIN_NO_ENZYME);
    2640     minNoEnzyme.setValue(omssaParameterSet.getMinNoEnzyme());
    2641     extraFS.add(minNoEnzyme);
    2642     // Extra, max no enzyme
    2643     TextField<String> maxNoEnzyme = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_MAX_NO_ENZYME);
    2644     maxNoEnzyme.setValue(omssaParameterSet.getMaxNoEnzyme());
    2645     extraFS.add(maxNoEnzyme);
    2646     // Extra, exact mass
    2647     TextField<String> exactMass = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_EXACT_MASS);
    2648     exactMass.setValue(omssaParameterSet.getExactMass());
    2649     extraFS.add(exactMass);
    2650     // Extra, setting id
    2651     TextField<String> settingId = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SETTING_ID);
    2652     settingId.setValue(omssaParameterSet.getSettingId());
    2653     extraFS.add(settingId);
    2654     // Extra, research threshold
    2655     TextField<String> researchThreshold = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_RESEARCH_THRESH);
    2656     researchThreshold.setValue(omssaParameterSet.getResearchThresh());
    2657     extraFS.add(researchThreshold);
    2658     // Extra, subset threshold
    2659     TextField<String> subsetThreshold = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_SUBSET_THRESH);
    2660     subsetThreshold.setValue(omssaParameterSet.getSubsetThresh());
    2661     extraFS.add(subsetThreshold);
    2662     // Extra, replace threshold
    2663     TextField<String> replaceThreshold = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_REPLACE_THRESH);
    2664     replaceThreshold.setValue(omssaParameterSet.getReplaceThresh());
    2665     extraFS.add(replaceThreshold);
    2666     // Extra, precursor cull
    2667     TextField<String> precursorCull = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PRECURSOR_CULL);
    2668     precursorCull.setValue(omssaParameterSet.getPrecursorCull());
    2669     extraFS.add(precursorCull);
    2670     // Extra, no correlation score
    2671     TextField<String> noCorrelationScore = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_NO_CORRELATION_SCORE);
    2672     noCorrelationScore.setValue(omssaParameterSet.getNoCorrelationScore());
    2673     extraFS.add(noCorrelationScore);
    2674     // Extra, prob following ion
    2675     TextField<String> probFollowingIon = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_PROB_FOLLOWING_ION);
    2676     probFollowingIon.setValue(omssaParameterSet.getProbFollowingIon());
    2677     extraFS.add(probFollowingIon);
    2678     // Extra, nMethionine
    2679     validStringParam = SaveOMSSAParameterSetStorage.VOMSSA_NMETHIONINE_ATTRIBUTE;
    2680     optionList = new ArrayList<Option>();
    2681     optionList.add(new Option("true", "true"));
    2682     optionList.add(new Option("false", "false"));
    2683     selected = omssaParameterSet.getNMethionineAttribute();
    2684     Select<VString> nMethionineSelectBox = new Select<VString>(validStringParam, optionList);
    2685   nMethionineSelectBox.selectOption( selected);
    2686     nMethionineSelectBox.setLabel("OMSSANMethionineSelect");
    2687     extraFS.add(nMethionineSelectBox);
    2688     // Extra, auto mass adjust
    2689     TextField<String> autoMassAdjust = new TextField<String>(SaveOMSSAParameterSetStorage.VOMSSA_AUTO_MASS_ADJUST);
    2690     autoMassAdjust.setValue(omssaParameterSet.getAutoMassAdjust());
    2691     extraFS.add(autoMassAdjust);
    2692     //
    2693     return form;
    2694   }
    26952290
    26962291
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