src/jalview/fts/service/uniprot/UniprotFTSPanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.fts.service.uniprot;
  23
  24 import jalview.fts.api.FTSDataColumnI;
  25 import jalview.fts.api.FTSRestClientI;
  26 import jalview.fts.core.FTSRestRequest;
  27 import jalview.fts.core.FTSRestResponse;
  28 import jalview.fts.core.GFTSPanel;
  29 import jalview.gui.SequenceFetcher;
  30 import jalview.util.MessageManager;
  31
  32 import java.util.HashMap;
  33 import java.util.HashSet;
  34 import java.util.Map;
  35
  36 @SuppressWarnings("serial")
  37 public class UniprotFTSPanel extends GFTSPanel
  38 {
  39
  40   private static String defaultFTSFrameTitle = MessageManager
  41           .getString("label.uniprot_sequence_fetcher");
  42
  43   private static Map<String, Integer> tempUserPrefs = new HashMap<>();
  44
  45   private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
  46
  47   private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
  48
  49   /**
  50    * Constructor given an (optional) sequence fetcher panel to revert to on
  51    * clicking the 'Back' button
  52    *
  53    * @param fetcher
  54    */
  55   public UniprotFTSPanel(SequenceFetcher fetcher)
  56   {
  57     super(fetcher);
  58     pageLimit = UniProtFTSRestClient.getInstance()
  59             .getDefaultResponsePageSize();
  60     this.seqFetcher = fetcher;
  61     this.progressIndicator = (fetcher == null) ? null
  62             : fetcher.getProgressIndicator();
  63   }
  64
  65   @Override
  66   public void searchAction(boolean isFreshSearch)
  67   {
  68     mainFrame.requestFocusInWindow();
  69     if (isFreshSearch)
  70     {
  71       offSet = 0;
  72     }
  73     new Thread()
  74     {
  75       @Override
  76       public void run()
  77       {
  78         reset();
  79         String searchInput = getTypedText();
  80         if (searchInput.length() > 0)
  81         {
  82           setSearchInProgress(true);
  83           long startTime = System.currentTimeMillis();
  84           searchInput = getTypedText();
  85           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  86                   .getSelectedItem()).getAltCode();
  87           wantedFields = UniProtFTSRestClient.getInstance()
  88                   .getAllDefaultDisplayedFTSDataColumns();
  89           String searchTerm = decodeSearchTerm(searchInput, searchTarget);
  90
  91           FTSRestRequest request = new FTSRestRequest();
  92           request.setFieldToSearchBy(searchTarget);
  93           request.setSearchTerm(searchTerm);
  94           request.setOffSet(offSet);
  95           request.setWantedFields(wantedFields);
  96           FTSRestClientI uniProtRestClient = UniProtFTSRestClient
  97                   .getInstance();
  98           FTSRestResponse resultList;
  99           try
 100           {
 101             resultList = uniProtRestClient.executeRequest(request);
 102           } catch (Exception e)
 103           {
 104             setErrorMessage(e.getMessage());
 105             checkForErrors();
 106             setSearchInProgress(false);
 107             return;
 108           }
 109
 110           if (resultList.getSearchSummary() != null
 111                   && resultList.getSearchSummary().size() > 0)
 112           {
 113             getResultTable().setModel(FTSRestResponse.getTableModel(request,
 114                     resultList.getSearchSummary()));
 115             FTSRestResponse.configureTableColumn(getResultTable(),
 116                     wantedFields, tempUserPrefs);
 117             getResultTable().setVisible(true);
 118           }
 119
 120           long endTime = System.currentTimeMillis();
 121           totalResultSetCount = resultList.getNumberOfItemsFound();
 122           resultSetCount = resultList.getSearchSummary() == null ? 0
 123                   : resultList.getSearchSummary().size();
 124           String result = (resultSetCount > 0)
 125                   ? MessageManager.getString("label.results")
 126                   : MessageManager.getString("label.result");
 127           if (isPaginationEnabled() && resultSetCount > 0)
 128           {
 129             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 130                     + " "
 131                     + totalNumberformatter
 132                             .format(Integer.valueOf(offSet + 1))
 133                     + " to "
 134                     + totalNumberformatter
 135                             .format(Integer
 136                                     .valueOf(offSet + resultSetCount))
 137                     + " of "
 138                     + totalNumberformatter
 139                             .format(Integer.valueOf(totalResultSetCount))
 140                     + " " + " (" + (endTime - startTime) + " milli secs)");
 141           }
 142           else
 143           {
 144             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 145                     + resultSetCount + " " + result + " ("
 146                     + (endTime - startTime) + " milli secs)");
 147           }
 148           setSearchInProgress(false);
 149           refreshPaginatorState();
 150           updateSummaryTableSelections();
 151         }
 152         txt_search.updateCache();
 153       }
 154     }.start();
 155
 156   }
 157
 158   public String decodeSearchTerm(String enteredText, String targetField)
 159   {
 160     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 161             : targetField.length() + 1;
 162     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 163             : targetField + ":";
 164     String foundSearchTerms = enteredText;
 165     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 166     if (enteredText.contains(";"))
 167     {
 168       String[] searchTerms = enteredText.split(";");
 169       for (String searchTerm : searchTerms)
 170       {
 171         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 172                 .append(" OR ");
 173       }
 174       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 175       foundSearchTerms = foundSearchTermsBuilder.toString();
 176       if (foundSearchTerms.contains(" OR "))
 177       {
 178         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 179                 endIndex);
 180       }
 181     }
 182     return foundSearchTerms;
 183   }
 184
 185   @Override
 186   public boolean isPaginationEnabled()
 187   {
 188     return true;
 189   }
 190
 191   @Override
 192   public void okAction()
 193   {
 194     disableActionButtons();
 195     StringBuilder selectedIds = new StringBuilder();
 196     HashSet<String> selectedIdsSet = new HashSet<>();
 197     int primaryKeyColIndex = 0;
 198     try
 199     {
 200       primaryKeyColIndex = getFTSRestClient()
 201               .getPrimaryKeyColumIndex(wantedFields, false);
 202     } catch (Exception e)
 203     {
 204       e.printStackTrace();
 205     }
 206     int[] selectedRows = getResultTable().getSelectedRows();
 207     for (int summaryRow : selectedRows)
 208     {
 209       String idStr = getResultTable()
 210               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 211       selectedIdsSet.add(idStr);
 212     }
 213     selectedIdsSet.addAll(paginatorCart);
 214     for (String selectedId : selectedIdsSet)
 215     {
 216       selectedIds.append(selectedId).append(";");
 217     }
 218
 219     String ids = selectedIds.toString();
 220     seqFetcher.setQuery(ids);
 221     Thread worker = new Thread(seqFetcher);
 222     worker.start();
 223     delayAndEnableActionButtons();
 224   }
 225
 226   @Override
 227   public FTSRestClientI getFTSRestClient()
 228   {
 229     return UniProtFTSRestClient.getInstance();
 230   }
 231
 232   @Override
 233   public String getFTSFrameTitle()
 234   {
 235     return defaultFTSFrameTitle;
 236   }
 237
 238   @Override
 239   public Map<String, Integer> getTempUserPrefs()
 240   {
 241     return tempUserPrefs;
 242   }
 243
 244   @Override
 245   public String getCacheKey()
 246   {
 247     return UNIPROT_FTS_CACHE_KEY;
 248   }
 249
 250   @Override
 251   public String getAutosearchPreference()
 252   {
 253     return UNIPROT_AUTOSEARCH;
 254   }
 255 }