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.Help;
  30 import jalview.gui.Help.HelpId;
  31 import jalview.gui.SequenceFetcher;
  32 import jalview.util.MessageManager;
  33
  34 import java.util.HashMap;
  35 import java.util.HashSet;
  36 import java.util.Map;
  37
  38 import javax.help.HelpSetException;
  39
  40 @SuppressWarnings("serial")
  41 public class UniprotFTSPanel extends GFTSPanel
  42 {
  43
  44   private static String defaultFTSFrameTitle = MessageManager
  45           .getString("label.uniprot_sequence_fetcher");
  46
  47   private static Map<String, Integer> tempUserPrefs = new HashMap<>();
  48
  49   private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
  50
  51   private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
  52
  53   /**
  54    * Constructor given an (optional) sequence fetcher panel to revert to on
  55    * clicking the 'Back' button
  56    *
  57    * @param fetcher
  58    */
  59   public UniprotFTSPanel(SequenceFetcher fetcher)
  60   {
  61     super(fetcher);
  62     pageLimit = UniProtFTSRestClient.getInstance()
  63             .getDefaultResponsePageSize();
  64     this.seqFetcher = fetcher;
  65     this.progressIndicator = (fetcher == null) ? null
  66             : fetcher.getProgressIndicator();
  67   }
  68
  69   @Override
  70   public void searchAction(boolean isFreshSearch)
  71   {
  72     mainFrame.requestFocusInWindow();
  73     if (isFreshSearch)
  74     {
  75       offSet = 0;
  76     }
  77     new Thread()
  78     {
  79       @Override
  80       public void run()
  81       {
  82         reset();
  83         String searchInput = getTypedText();
  84         if (searchInput.length() > 0)
  85         {
  86           setSearchInProgress(true);
  87           long startTime = System.currentTimeMillis();
  88           searchInput = getTypedText();
  89           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  90                   .getSelectedItem()).getAltCode();
  91           wantedFields = UniProtFTSRestClient.getInstance()
  92                   .getAllDefaultDisplayedFTSDataColumns();
  93           String searchTerm = decodeSearchTerm(searchInput, searchTarget);
  94
  95           FTSRestRequest request = new FTSRestRequest();
  96           request.setFieldToSearchBy(searchTarget);
  97           request.setSearchTerm(searchTerm);
  98           request.setOffSet(offSet);
  99           request.setWantedFields(wantedFields);
 100           FTSRestClientI uniProtRestClient = UniProtFTSRestClient
 101                   .getInstance();
 102           FTSRestResponse resultList;
 103           try
 104           {
 105             resultList = uniProtRestClient.executeRequest(request);
 106           } catch (Exception e)
 107           {
 108             setErrorMessage(e.getMessage());
 109             checkForErrors();
 110             setSearchInProgress(false);
 111             return;
 112           }
 113
 114           if (resultList.getSearchSummary() != null
 115                   && resultList.getSearchSummary().size() > 0)
 116           {
 117             getResultTable().setModel(FTSRestResponse.getTableModel(request,
 118                     resultList.getSearchSummary()));
 119             FTSRestResponse.configureTableColumn(getResultTable(),
 120                     wantedFields, tempUserPrefs);
 121             getResultTable().setVisible(true);
 122           }
 123
 124           long endTime = System.currentTimeMillis();
 125           totalResultSetCount = resultList.getNumberOfItemsFound();
 126           resultSetCount = resultList.getSearchSummary() == null ? 0
 127                   : resultList.getSearchSummary().size();
 128           String result = (resultSetCount > 0)
 129                   ? MessageManager.getString("label.results")
 130                   : MessageManager.getString("label.result");
 131           if (isPaginationEnabled() && resultSetCount > 0)
 132           {
 133             updateSearchFrameTitle(
 134                     defaultFTSFrameTitle + " - " + result + " "
 135                             + totalNumberformatter
 136                                     .format(Integer.valueOf(offSet + 1))
 137                             + " to "
 138                             + totalNumberformatter.format(Integer
 139                                     .valueOf(offSet + resultSetCount))
 140                             + " of "
 141                             + totalNumberformatter.format(
 142                                     Integer.valueOf(totalResultSetCount))
 143                             + " " + " (" + (endTime - startTime)
 144                             + " milli secs)");
 145           }
 146           else
 147           {
 148             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 149                     + resultSetCount + " " + result + " ("
 150                     + (endTime - startTime) + " milli secs)");
 151           }
 152           setSearchInProgress(false);
 153           refreshPaginatorState();
 154           updateSummaryTableSelections();
 155         }
 156         txt_search.updateCache();
 157       }
 158     }.start();
 159
 160   }
 161
 162   public String decodeSearchTerm(String enteredText, String targetField)
 163   {
 164     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 165             : targetField.length() + 1;
 166     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 167             : targetField + ":";
 168     String foundSearchTerms = enteredText;
 169     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 170     if (enteredText.contains(";"))
 171     {
 172       String[] searchTerms = enteredText.split(";");
 173       for (String searchTerm : searchTerms)
 174       {
 175         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 176                 .append(" OR ");
 177       }
 178       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 179       foundSearchTerms = foundSearchTermsBuilder.toString();
 180       if (foundSearchTerms.contains(" OR "))
 181       {
 182         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 183                 endIndex);
 184       }
 185     }
 186     return foundSearchTerms;
 187   }
 188
 189   @Override
 190   public boolean isPaginationEnabled()
 191   {
 192     return true;
 193   }
 194
 195   @Override
 196   public void okAction()
 197   {
 198     disableActionButtons();
 199     StringBuilder selectedIds = new StringBuilder();
 200     HashSet<String> selectedIdsSet = new HashSet<>();
 201     int primaryKeyColIndex = 0;
 202     try
 203     {
 204       primaryKeyColIndex = getFTSRestClient()
 205               .getPrimaryKeyColumIndex(wantedFields, false);
 206     } catch (Exception e)
 207     {
 208       e.printStackTrace();
 209     }
 210     int[] selectedRows = getResultTable().getSelectedRows();
 211     for (int summaryRow : selectedRows)
 212     {
 213       String idStr = getResultTable()
 214               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 215       selectedIdsSet.add(idStr);
 216     }
 217     selectedIdsSet.addAll(paginatorCart);
 218     for (String selectedId : selectedIdsSet)
 219     {
 220       selectedIds.append(selectedId).append(";");
 221     }
 222
 223     String ids = selectedIds.toString();
 224     seqFetcher.setQuery(ids);
 225     Thread worker = new Thread(seqFetcher);
 226     worker.start();
 227     delayAndEnableActionButtons();
 228   }
 229
 230   @Override
 231   public FTSRestClientI getFTSRestClient()
 232   {
 233     return UniProtFTSRestClient.getInstance();
 234   }
 235
 236   @Override
 237   public String getFTSFrameTitle()
 238   {
 239     return defaultFTSFrameTitle;
 240   }
 241
 242   @Override
 243   public Map<String, Integer> getTempUserPrefs()
 244   {
 245     return tempUserPrefs;
 246   }
 247
 248   @Override
 249   public String getCacheKey()
 250   {
 251     return UNIPROT_FTS_CACHE_KEY;
 252   }
 253
 254   @Override
 255   public String getAutosearchPreference()
 256   {
 257     return UNIPROT_AUTOSEARCH;
 258   }
 259
 260   @Override
 261   protected void showHelp()
 262   {
 263     try
 264     {
 265       Help.showHelpWindow(HelpId.UniprotFts);
 266     } catch (HelpSetException e1)
 267     {
 268       e1.printStackTrace();
 269     }
 270   }
 271 }