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     initCache();
  57   }
  58
  59   @Override
  60   public void searchAction(boolean isFreshSearch)
  61   {
  62     if (isFreshSearch)
  63     {
  64       offSet = 0;
  65     }
  66     new Thread()
  67     {
  68       @Override
  69       public void run()
  70       {
  71         reset();
  72         String searchInput = getTypedText();
  73         if (searchInput.length() > 0)
  74         {
  75           setSearchInProgress(true);
  76           long startTime = System.currentTimeMillis();
  77           searchInput = getTypedText();
  78           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  79                   .getSelectedItem()).getAltCode();
  80           wantedFields = UniProtFTSRestClient.getInstance()
  81                   .getAllDefaultDisplayedFTSDataColumns();
  82           String searchTerm = decodeSearchTerm(searchInput, searchTarget);
  83
  84           FTSRestRequest request = new FTSRestRequest();
  85           request.setFieldToSearchBy(searchTarget);
  86           request.setSearchTerm(searchTerm);
  87           request.setOffSet(offSet);
  88           request.setWantedFields(wantedFields);
  89           FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
  90                   .getInstance();
  91           FTSRestResponse resultList;
  92           try
  93           {
  94             resultList = uniProtRestCleint.executeRequest(request);
  95           } catch (Exception e)
  96           {
  97             e.printStackTrace();
  98             setErrorMessage(e.getMessage());
  99             checkForErrors();
 100             return;
 101           }
 102
 103           if (resultList.getSearchSummary() != null
 104                   && resultList.getSearchSummary().size() > 0)
 105           {
 106             getResultTable().setModel(
 107                     FTSRestResponse.getTableModel(request,
 108                             resultList.getSearchSummary()));
 109             FTSRestResponse.configureTableColumn(getResultTable(),
 110                     wantedFields, tempUserPrefs);
 111             getResultTable().setVisible(true);
 112           }
 113
 114           long endTime = System.currentTimeMillis();
 115           totalResultSetCount = resultList.getNumberOfItemsFound();
 116           resultSetCount = resultList.getSearchSummary() == null ? 0
 117                   : resultList.getSearchSummary().size();
 118           String result = (resultSetCount > 0) ? MessageManager
 119                   .getString("label.results") : MessageManager
 120                   .getString("label.result");
 121           if (isPaginationEnabled() && resultSetCount > 0)
 122           {
 123             updateSearchFrameTitle(defaultFTSFrameTitle
 124                     + " - "
 125                     + result
 126                     + " "
 127                     + totalNumberformatter.format((Number) (offSet + 1))
 128                     + " to "
 129                     + totalNumberformatter
 130                             .format((Number) (offSet + resultSetCount))
 131                     + " of "
 132                     + totalNumberformatter
 133                             .format((Number) totalResultSetCount) + " "
 134                     + " (" + (endTime - startTime) + " milli secs)");
 135           }
 136           else
 137           {
 138             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 139                     + resultSetCount + " " + result + " ("
 140                     + (endTime - startTime) + " milli secs)");
 141           }
 142           setSearchInProgress(false);
 143           refreshPaginatorState();
 144           updateSummaryTableSelections();
 145           updateCache();
 146         }
 147       }
 148     }.start();
 149
 150   }
 151
 152   public String decodeSearchTerm(String enteredText, String targetField)
 153   {
 154     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 155             : targetField.length() + 1;
 156     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 157             : targetField + ":";
 158     String foundSearchTerms = enteredText;
 159     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 160     if (enteredText.contains(";"))
 161     {
 162       String[] searchTerms = enteredText.split(";");
 163       for (String searchTerm : searchTerms)
 164       {
 165         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 166                 .append(" OR ");
 167       }
 168       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 169       foundSearchTerms = foundSearchTermsBuilder.toString();
 170       if (foundSearchTerms.contains(" OR "))
 171       {
 172         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 173                 endIndex);
 174       }
 175     }
 176     return foundSearchTerms;
 177   }
 178
 179   @Override
 180   public boolean isPaginationEnabled()
 181   {
 182     return true;
 183   }
 184
 185   @Override
 186   public void okAction()
 187   {
 188     disableActionButtons();
 189     StringBuilder selectedIds = new StringBuilder();
 190     HashSet<String> selectedIdsSet = new HashSet<String>();
 191     int primaryKeyColIndex = 0;
 192     try
 193     {
 194       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 195               wantedFields, false);
 196     } catch (Exception e)
 197     {
 198       e.printStackTrace();
 199     }
 200     int[] selectedRows = getResultTable().getSelectedRows();
 201     for (int summaryRow : selectedRows)
 202     {
 203       String idStr = getResultTable().getValueAt(summaryRow,
 204               primaryKeyColIndex).toString();
 205       selectedIdsSet.add(idStr);
 206     }
 207     selectedIdsSet.addAll(paginatorCart);
 208     for (String selectedId : selectedIdsSet)
 209     {
 210       selectedIds.append(selectedId).append(";");
 211     }
 212
 213     String ids = selectedIds.toString();
 214     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 215     seqFetcher.getTextArea().setText(ids);
 216     Thread worker = new Thread(seqFetcher);
 217     worker.start();
 218     delayAndEnableActionButtons();
 219   }
 220
 221   @Override
 222   public FTSRestClientI getFTSRestClient()
 223   {
 224     return UniProtFTSRestClient.getInstance();
 225   }
 226
 227   @Override
 228   public String getFTSFrameTitle()
 229   {
 230     return defaultFTSFrameTitle;
 231   }
 232
 233   @Override
 234   public Map<String, Integer> getTempUserPrefs()
 235   {
 236     return tempUserPrefs;
 237   }
 238
 239   @Override
 240   public String getCacheKey()
 241   {
 242     return UNIPROT_FTS_CACHE_KEY;
 243   }
 244 }