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.HashSet;
  33
  34 @SuppressWarnings("serial")
  35 public class UniprotFTSPanel extends GFTSPanel
  36 {
  37
  38   private static String defaultFTSFrameTitle = MessageManager
  39           .getString("label.uniprot_sequence_fetcher");
  40
  41   private String ftsFrameTitle = defaultFTSFrameTitle;
  42
  43
  44
  45   public UniprotFTSPanel(SequenceFetcher seqFetcher)
  46   {
  47     pageLimit = UniProtFTSRestClient.getInstance()
  48             .getDefaultResponsePageSize();
  49     this.seqFetcher = seqFetcher;
  50     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  51             .getProgressIndicator();
  52   }
  53
  54   @Override
  55   public void searchAction(boolean isFreshSearch)
  56   {
  57     if (isFreshSearch)
  58     {
  59       offSet = 0;
  60     }
  61     new Thread()
  62   {
  63       @Override
  64       public void run()
  65       {
  66         ftsFrameTitle = defaultFTSFrameTitle;
  67         reset();
  68         if (getTypedText().length() > 0)
  69         {
  70           setSearchInProgress(true);
  71           long startTime = System.currentTimeMillis();
  72
  73           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  74                   .getSelectedItem()).getAltCode();
  75
  76           wantedFields = UniProtFTSRestClient.getInstance()
  77                   .getAllDefaultDisplayedFTSDataColumns();
  78           String searchTerm = decodeSearchTerm(txt_search.getText(),
  79                   searchTarget);
  80
  81           FTSRestRequest request = new FTSRestRequest();
  82           request.setFieldToSearchBy(searchTarget);
  83           request.setSearchTerm(searchTerm);
  84           request.setOffSet(offSet);
  85           request.setWantedFields(wantedFields);
  86           FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
  87                   .getInstance();
  88           FTSRestResponse resultList;
  89           try
  90           {
  91             resultList = uniProtRestCleint.executeRequest(request);
  92           } catch (Exception e)
  93           {
  94             e.printStackTrace();
  95             setErrorMessage(e.getMessage());
  96             checkForErrors();
  97             return;
  98           }
  99
 100           if (resultList.getSearchSummary() != null
 101                   && resultList.getSearchSummary().size() > 0)
 102           {
 103             getResultTable().setModel(
 104                     FTSRestResponse.getTableModel(request,
 105                             resultList.getSearchSummary()));
 106             FTSRestResponse.configureTableColumn(getResultTable(),
 107                     wantedFields);
 108             getResultTable().setVisible(true);
 109           }
 110
 111           long endTime = System.currentTimeMillis();
 112           totalResultSetCount = resultList.getNumberOfItemsFound();
 113           resultSetCount = resultList.getSearchSummary() == null ? 0
 114                   : resultList.getSearchSummary().size();
 115           String result = (resultSetCount > 0) ? MessageManager
 116                   .getString("label.results") : MessageManager
 117                   .getString("label.result");
 118           if (isPaginationEnabled() && resultSetCount > 0)
 119           {
 120             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 121                     + " "
 122                     + totalNumberformatter.format((Number) (offSet + 1))
 123                     + " to "
 124                     + totalNumberformatter
 125                             .format((Number) (offSet + resultSetCount))
 126                     + " of "
 127                     + totalNumberformatter
 128                             .format((Number) totalResultSetCount)
 129                     + " " + " (" + (endTime - startTime) + " milli secs)");
 130           }
 131           else
 132           {
 133             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 134                     + resultSetCount + " " + result + " ("
 135                     + (endTime - startTime) + " milli secs)");
 136           }
 137           setSearchInProgress(false);
 138           refreshPaginatorState();
 139           updateSummaryTableSelections();
 140         }
 141       }
 142     }.start();
 143
 144   }
 145
 146   public String decodeSearchTerm(String enteredText, String targetField)
 147   {
 148     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 149             : targetField.length() + 1;
 150     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 151             : targetField + ":";
 152     String foundSearchTerms = enteredText;
 153     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 154     if (enteredText.contains(";"))
 155     {
 156       String[] searchTerms = enteredText.split(";");
 157       for (String searchTerm : searchTerms)
 158       {
 159         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 160                 .append(" OR ");
 161       }
 162       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 163       foundSearchTerms = foundSearchTermsBuilder.toString();
 164       if (foundSearchTerms.contains(" OR "))
 165       {
 166         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 167                 endIndex);
 168       }
 169     }
 170     return foundSearchTerms;
 171   }
 172
 173
 174   @Override
 175   public boolean isPaginationEnabled()
 176   {
 177     return true;
 178   }
 179
 180   @Override
 181   public void okAction()
 182   {
 183     disableActionButtons();
 184     StringBuilder selectedIds = new StringBuilder();
 185     HashSet<String> selectedIdsSet = new HashSet<String>();
 186     int primaryKeyColIndex = 0;
 187     try
 188     {
 189       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 190               wantedFields, false);
 191     } catch (Exception e)
 192     {
 193       e.printStackTrace();
 194     }
 195     int[] selectedRows = getResultTable().getSelectedRows();
 196     for (int summaryRow : selectedRows)
 197     {
 198       String idStr = getResultTable().getValueAt(summaryRow,
 199               primaryKeyColIndex).toString();
 200       selectedIdsSet.add(idStr);
 201     }
 202     selectedIdsSet.addAll(paginatorCart);
 203     for (String selectedId : selectedIdsSet)
 204     {
 205       selectedIds.append(selectedId).append(";");
 206     }
 207
 208     String ids = selectedIds.toString();
 209     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 210     seqFetcher.getTextArea().setText(ids);
 211     Thread worker = new Thread(seqFetcher);
 212     worker.start();
 213     delayAndEnableActionButtons();
 214   }
 215
 216   @Override
 217   public FTSRestClientI getFTSRestClient()
 218   {
 219     return UniProtFTSRestClient.getInstance();
 220   }
 221
 222   @Override
 223   public String getFTSFrameTitle()
 224   {
 225     return ftsFrameTitle;
 226   }
 227
 228 }