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
  44   private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
  45
  46   private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
  47
  48   public UniprotFTSPanel(SequenceFetcher seqFetcher)
  49   {
  50     super();
  51     pageLimit = UniProtFTSRestClient.getInstance()
  52             .getDefaultResponsePageSize();
  53     this.seqFetcher = seqFetcher;
  54     this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
  55             .getProgressIndicator();
  56   }
  57
  58   @Override
  59   public void searchAction(boolean isFreshSearch)
  60   {
  61     if (isFreshSearch)
  62     {
  63       offSet = 0;
  64     }
  65     new Thread()
  66     {
  67       @Override
  68       public void run()
  69       {
  70         reset();
  71         String searchInput = getTypedText();
  72         if (searchInput.length() > 0)
  73         {
  74           setSearchInProgress(true);
  75           long startTime = System.currentTimeMillis();
  76           searchInput = getTypedText();
  77           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  78                   .getSelectedItem()).getAltCode();
  79           wantedFields = UniProtFTSRestClient.getInstance()
  80                   .getAllDefaultDisplayedFTSDataColumns();
  81           String searchTerm = decodeSearchTerm(searchInput, searchTarget);
  82
  83           FTSRestRequest request = new FTSRestRequest();
  84           request.setFieldToSearchBy(searchTarget);
  85           request.setSearchTerm(searchTerm);
  86           request.setOffSet(offSet);
  87           request.setWantedFields(wantedFields);
  88           FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
  89                   .getInstance();
  90           FTSRestResponse resultList;
  91           try
  92           {
  93             resultList = uniProtRestCleint.executeRequest(request);
  94           } catch (Exception e)
  95           {
  96             e.printStackTrace();
  97             setErrorMessage(e.getMessage());
  98             checkForErrors();
  99             return;
 100           }
 101
 102           if (resultList.getSearchSummary() != null
 103                   && resultList.getSearchSummary().size() > 0)
 104           {
 105             getResultTable().setModel(
 106                     FTSRestResponse.getTableModel(request,
 107                             resultList.getSearchSummary()));
 108             FTSRestResponse.configureTableColumn(getResultTable(),
 109                     wantedFields, tempUserPrefs);
 110             getResultTable().setVisible(true);
 111           }
 112
 113           long endTime = System.currentTimeMillis();
 114           totalResultSetCount = resultList.getNumberOfItemsFound();
 115           resultSetCount = resultList.getSearchSummary() == null ? 0
 116                   : resultList.getSearchSummary().size();
 117           String result = (resultSetCount > 0) ? MessageManager
 118                   .getString("label.results") : MessageManager
 119                   .getString("label.result");
 120           if (isPaginationEnabled() && resultSetCount > 0)
 121           {
 122             updateSearchFrameTitle(defaultFTSFrameTitle
 123                     + " - "
 124                     + result
 125                     + " "
 126                     + totalNumberformatter.format((Number) (offSet + 1))
 127                     + " to "
 128                     + totalNumberformatter
 129                             .format((Number) (offSet + resultSetCount))
 130                     + " of "
 131                     + totalNumberformatter
 132                             .format((Number) totalResultSetCount) + " "
 133                     + " (" + (endTime - startTime) + " milli secs)");
 134           }
 135           else
 136           {
 137             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 138                     + resultSetCount + " " + result + " ("
 139                     + (endTime - startTime) + " milli secs)");
 140           }
 141           setSearchInProgress(false);
 142           refreshPaginatorState();
 143           updateSummaryTableSelections();
 144         }
 145         txt_search.updateCache();
 146       }
 147     }.start();
 148
 149   }
 150
 151   public String decodeSearchTerm(String enteredText, String targetField)
 152   {
 153     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 154             : targetField.length() + 1;
 155     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 156             : targetField + ":";
 157     String foundSearchTerms = enteredText;
 158     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 159     if (enteredText.contains(";"))
 160     {
 161       String[] searchTerms = enteredText.split(";");
 162       for (String searchTerm : searchTerms)
 163       {
 164         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 165                 .append(" OR ");
 166       }
 167       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 168       foundSearchTerms = foundSearchTermsBuilder.toString();
 169       if (foundSearchTerms.contains(" OR "))
 170       {
 171         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 172                 endIndex);
 173       }
 174     }
 175     return foundSearchTerms;
 176   }
 177
 178   @Override
 179   public boolean isPaginationEnabled()
 180   {
 181     return true;
 182   }
 183
 184   @Override
 185   public void okAction()
 186   {
 187     disableActionButtons();
 188     StringBuilder selectedIds = new StringBuilder();
 189     HashSet<String> selectedIdsSet = new HashSet<String>();
 190     int primaryKeyColIndex = 0;
 191     try
 192     {
 193       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 194               wantedFields, false);
 195     } catch (Exception e)
 196     {
 197       e.printStackTrace();
 198     }
 199     int[] selectedRows = getResultTable().getSelectedRows();
 200     for (int summaryRow : selectedRows)
 201     {
 202       String idStr = getResultTable().getValueAt(summaryRow,
 203               primaryKeyColIndex).toString();
 204       selectedIdsSet.add(idStr);
 205     }
 206     selectedIdsSet.addAll(paginatorCart);
 207     for (String selectedId : selectedIdsSet)
 208     {
 209       selectedIds.append(selectedId).append(";");
 210     }
 211
 212     String ids = selectedIds.toString();
 213     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 214     seqFetcher.getTextArea().setText(ids);
 215     Thread worker = new Thread(seqFetcher);
 216     worker.start();
 217     delayAndEnableActionButtons();
 218   }
 219
 220   @Override
 221   public FTSRestClientI getFTSRestClient()
 222   {
 223     return UniProtFTSRestClient.getInstance();
 224   }
 225
 226   @Override
 227   public String getFTSFrameTitle()
 228   {
 229     return defaultFTSFrameTitle;
 230   }
 231
 232   @Override
 233   public Map<String, Integer> getTempUserPrefs()
 234   {
 235     return tempUserPrefs;
 236   }
 237
 238   @Override
 239   public String getCacheKey()
 240   {
 241     return UNIPROT_FTS_CACHE_KEY;
 242   }
 243 }