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 seqFetcher)
  48   {
  49     super();
  50     pageLimit = UniProtFTSRestClient.getInstance()
  51             .getDefaultResponsePageSize();
  52     this.seqFetcher = seqFetcher;
  53     this.progressIndicator = (seqFetcher == null) ? null
  54             : seqFetcher.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 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             setSearchInProgress(false);
 100             return;
 101           }
 102
 103           if (resultList.getSearchSummary() != null
 104                   && resultList.getSearchSummary().size() > 0)
 105           {
 106             getResultTable().setModel(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)
 118                   ? MessageManager.getString("label.results")
 119                   : MessageManager.getString("label.result");
 120           if (isPaginationEnabled() && resultSetCount > 0)
 121           {
 122             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 123                     + " "
 124                     + totalNumberformatter.format((Number) (offSet + 1))
 125                     + " to "
 126                     + totalNumberformatter
 127                             .format((Number) (offSet + resultSetCount))
 128                     + " of "
 129                     + totalNumberformatter
 130                             .format((Number) totalResultSetCount)
 131                     + " " + " (" + (endTime - startTime) + " milli secs)");
 132           }
 133           else
 134           {
 135             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 136                     + resultSetCount + " " + result + " ("
 137                     + (endTime - startTime) + " milli secs)");
 138           }
 139           setSearchInProgress(false);
 140           refreshPaginatorState();
 141           updateSummaryTableSelections();
 142         }
 143         txt_search.updateCache();
 144       }
 145     }.start();
 146
 147   }
 148
 149   public String decodeSearchTerm(String enteredText, String targetField)
 150   {
 151     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 152             : targetField.length() + 1;
 153     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 154             : targetField + ":";
 155     String foundSearchTerms = enteredText;
 156     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 157     if (enteredText.contains(";"))
 158     {
 159       String[] searchTerms = enteredText.split(";");
 160       for (String searchTerm : searchTerms)
 161       {
 162         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 163                 .append(" OR ");
 164       }
 165       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 166       foundSearchTerms = foundSearchTermsBuilder.toString();
 167       if (foundSearchTerms.contains(" OR "))
 168       {
 169         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 170                 endIndex);
 171       }
 172     }
 173     return foundSearchTerms;
 174   }
 175
 176   @Override
 177   public boolean isPaginationEnabled()
 178   {
 179     return true;
 180   }
 181
 182   @Override
 183   public void okAction()
 184   {
 185     disableActionButtons();
 186     StringBuilder selectedIds = new StringBuilder();
 187     HashSet<String> selectedIdsSet = new HashSet<>();
 188     int primaryKeyColIndex = 0;
 189     try
 190     {
 191       primaryKeyColIndex = getFTSRestClient()
 192               .getPrimaryKeyColumIndex(wantedFields, false);
 193     } catch (Exception e)
 194     {
 195       e.printStackTrace();
 196     }
 197     int[] selectedRows = getResultTable().getSelectedRows();
 198     for (int summaryRow : selectedRows)
 199     {
 200       String idStr = getResultTable()
 201               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 202       selectedIdsSet.add(idStr);
 203     }
 204     selectedIdsSet.addAll(paginatorCart);
 205     for (String selectedId : selectedIdsSet)
 206     {
 207       selectedIds.append(selectedId).append(";");
 208     }
 209
 210     String ids = selectedIds.toString();
 211     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 212     seqFetcher.getTextArea().setText(ids);
 213     Thread worker = new Thread(seqFetcher);
 214     worker.start();
 215     delayAndEnableActionButtons();
 216   }
 217
 218   @Override
 219   public FTSRestClientI getFTSRestClient()
 220   {
 221     return UniProtFTSRestClient.getInstance();
 222   }
 223
 224   @Override
 225   public String getFTSFrameTitle()
 226   {
 227     return defaultFTSFrameTitle;
 228   }
 229
 230   @Override
 231   public Map<String, Integer> getTempUserPrefs()
 232   {
 233     return tempUserPrefs;
 234   }
 235
 236   @Override
 237   public String getCacheKey()
 238   {
 239     return UNIPROT_FTS_CACHE_KEY;
 240   }
 241 }