src/jalview/fts/service/pdb/PDBFTSPanel.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.pdb;
  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 PDBFTSPanel extends GFTSPanel
  38 {
  39   private static String defaultFTSFrameTitle = MessageManager
  40           .getString("label.pdb_sequence_fetcher");
  41
  42   private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
  43
  44   private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
  45
  46   public PDBFTSPanel(SequenceFetcher seqFetcher)
  47   {
  48     super();
  49     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
  50     this.seqFetcher = seqFetcher;
  51     this.progressIndicator = (seqFetcher == null) ? null
  52             : seqFetcher.getProgressIndicator();
  53   }
  54
  55   @Override
  56   public void searchAction(boolean isFreshSearch)
  57   {
  58     mainFrame.requestFocusInWindow();
  59     if (isFreshSearch)
  60     {
  61       offSet = 0;
  62     }
  63     new Thread()
  64     {
  65       @Override
  66       public void run()
  67       {
  68         reset();
  69         boolean allowEmptySequence = false;
  70         if (getTypedText().length() > 0)
  71         {
  72           setSearchInProgress(true);
  73           long startTime = System.currentTimeMillis();
  74
  75           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  76                   .getSelectedItem()).getCode();
  77           wantedFields = PDBFTSRestClient.getInstance()
  78                   .getAllDefaultDisplayedFTSDataColumns();
  79           String searchTerm = decodeSearchTerm(getTypedText(),
  80                   searchTarget);
  81
  82           FTSRestRequest request = new FTSRestRequest();
  83           request.setAllowEmptySeq(allowEmptySequence);
  84           request.setResponseSize(100);
  85           request.setFieldToSearchBy("(" + searchTarget + ":");
  86           request.setSearchTerm(searchTerm + ")");
  87           request.setOffSet(offSet);
  88           request.setWantedFields(wantedFields);
  89           FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
  90           FTSRestResponse resultList;
  91           try
  92           {
  93             resultList = pdbRestCleint.executeRequest(request);
  94           } catch (Exception e)
  95           {
  96             setErrorMessage(e.getMessage());
  97             checkForErrors();
  98             return;
  99           }
 100
 101           if (resultList.getSearchSummary() != null
 102                   && resultList.getSearchSummary().size() > 0)
 103           {
 104             getResultTable().setModel(FTSRestResponse.getTableModel(request,
 105                     resultList.getSearchSummary()));
 106             FTSRestResponse.configureTableColumn(getResultTable(),
 107                     wantedFields, tempUserPrefs);
 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)
 116                   ? MessageManager.getString("label.results")
 117                   : MessageManager.getString("label.result");
 118
 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
 139           setSearchInProgress(false);
 140           refreshPaginatorState();
 141           updateSummaryTableSelections();
 142         }
 143         txt_search.updateCache();
 144       }
 145     }.start();
 146   }
 147
 148   public static String decodeSearchTerm(String enteredText,
 149           String targetField)
 150   {
 151     String foundSearchTerms = enteredText;
 152     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 153     if (enteredText.contains(";"))
 154     {
 155       String[] searchTerms = enteredText.split(";");
 156       for (String searchTerm : searchTerms)
 157       {
 158         if (searchTerm.contains(":"))
 159         {
 160           foundSearchTermsBuilder.append(targetField).append(":")
 161                   .append(searchTerm.split(":")[0]).append(" OR ");
 162         }
 163         else
 164         {
 165           foundSearchTermsBuilder.append(targetField).append(":")
 166                   .append(searchTerm).append(" OR ");
 167         }
 168       }
 169       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 170       foundSearchTerms = foundSearchTermsBuilder.toString();
 171       if (foundSearchTerms.contains(" OR "))
 172       {
 173         foundSearchTerms = foundSearchTerms
 174                 .substring(targetField.length() + 1, endIndex);
 175       }
 176     }
 177     else if (enteredText.contains(":"))
 178     {
 179       foundSearchTerms = foundSearchTerms.split(":")[0];
 180     }
 181     return foundSearchTerms;
 182   }
 183
 184   @Override
 185   public void okAction()
 186   {
 187     // mainFrame.dispose();
 188     disableActionButtons();
 189     StringBuilder selectedIds = new StringBuilder();
 190     HashSet<String> selectedIdsSet = new HashSet<String>();
 191     int primaryKeyColIndex = 0;
 192     try
 193     {
 194       primaryKeyColIndex = getFTSRestClient()
 195               .getPrimaryKeyColumIndex(wantedFields, false);
 196     } catch (Exception e)
 197     {
 198       e.printStackTrace();
 199     }
 200     int[] selectedRows = getResultTable().getSelectedRows();
 201     String searchTerm = getTypedText();
 202     for (int summaryRow : selectedRows)
 203     {
 204       String idStr = getResultTable()
 205               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 206       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 207     }
 208
 209     for (String idStr : paginatorCart)
 210     {
 211       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 212     }
 213
 214     for (String selectedId : selectedIdsSet)
 215     {
 216       selectedIds.append(selectedId).append(";");
 217     }
 218
 219     String ids = selectedIds.toString();
 220     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 221     seqFetcher.getTextArea().setText(ids);
 222     Thread worker = new Thread(seqFetcher);
 223     worker.start();
 224     delayAndEnableActionButtons();
 225   }
 226
 227   public static String getPDBIdwithSpecifiedChain(String pdbId,
 228           String searchTerm)
 229   {
 230     String pdbIdWithChainCode = "";
 231     if (searchTerm.contains(";"))
 232     {
 233       String[] foundTerms = searchTerm.split(";");
 234       for (String foundTerm : foundTerms)
 235       {
 236         if (foundTerm.contains(pdbId))
 237         {
 238           pdbIdWithChainCode = foundTerm;
 239         }
 240       }
 241     }
 242     else if (searchTerm.contains(pdbId))
 243     {
 244       pdbIdWithChainCode = searchTerm;
 245     }
 246     else
 247     {
 248       pdbIdWithChainCode = pdbId;
 249     }
 250     return pdbIdWithChainCode;
 251   }
 252
 253   @Override
 254   public FTSRestClientI getFTSRestClient()
 255   {
 256     return PDBFTSRestClient.getInstance();
 257   }
 258
 259   @Override
 260   public String getFTSFrameTitle()
 261   {
 262     return defaultFTSFrameTitle;
 263   }
 264
 265   @Override
 266   public boolean isPaginationEnabled()
 267   {
 268     return true;
 269   }
 270
 271   @Override
 272   public Map<String, Integer> getTempUserPrefs()
 273   {
 274     return tempUserPrefs;
 275   }
 276
 277   @Override
 278   public String getCacheKey()
 279   {
 280     return PDB_FTS_CACHE_KEY;
 281   }
 282
 283 }