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