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 fetcher)
  47   {
  48     super();
  49     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
  50     this.seqFetcher = fetcher;
  51     this.progressIndicator = (fetcher == null) ? null
  52             : fetcher.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 pdbRestClient = PDBFTSRestClient.getInstance();
  90           FTSRestResponse resultList;
  91           try
  92           {
  93             resultList = pdbRestClient.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
 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
 140           setSearchInProgress(false);
 141           refreshPaginatorState();
 142           updateSummaryTableSelections();
 143         }
 144         txt_search.updateCache();
 145       }
 146     }.start();
 147   }
 148
 149   public static String decodeSearchTerm(String enteredText,
 150           String targetField)
 151   {
 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         if (searchTerm.contains(":"))
 160         {
 161           foundSearchTermsBuilder.append(targetField).append(":")
 162                   .append(searchTerm.split(":")[0]).append(" OR ");
 163         }
 164         else
 165         {
 166           foundSearchTermsBuilder.append(targetField).append(":")
 167                   .append(searchTerm).append(" OR ");
 168         }
 169       }
 170       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 171       foundSearchTerms = foundSearchTermsBuilder.toString();
 172       if (foundSearchTerms.contains(" OR "))
 173       {
 174         foundSearchTerms = foundSearchTerms
 175                 .substring(targetField.length() + 1, endIndex);
 176       }
 177     }
 178     else if (enteredText.contains(":"))
 179     {
 180       foundSearchTerms = foundSearchTerms.split(":")[0];
 181     }
 182     return foundSearchTerms;
 183   }
 184
 185   @Override
 186   public void okAction()
 187   {
 188     // mainFrame.dispose();
 189     disableActionButtons();
 190     StringBuilder selectedIds = new StringBuilder();
 191     HashSet<String> selectedIdsSet = new HashSet<String>();
 192     int primaryKeyColIndex = 0;
 193     try
 194     {
 195       primaryKeyColIndex = getFTSRestClient()
 196               .getPrimaryKeyColumIndex(wantedFields, false);
 197     } catch (Exception e)
 198     {
 199       e.printStackTrace();
 200     }
 201     int[] selectedRows = getResultTable().getSelectedRows();
 202     String searchTerm = getTypedText();
 203     for (int summaryRow : selectedRows)
 204     {
 205       String idStr = getResultTable()
 206               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 207       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 208     }
 209
 210     for (String idStr : paginatorCart)
 211     {
 212       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 213     }
 214
 215     for (String selectedId : selectedIdsSet)
 216     {
 217       selectedIds.append(selectedId).append(";");
 218     }
 219
 220     String ids = selectedIds.toString();
 221     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 222     seqFetcher.getTextArea().setText(ids);
 223     Thread worker = new Thread(seqFetcher);
 224     worker.start();
 225     delayAndEnableActionButtons();
 226   }
 227
 228   public static String getPDBIdwithSpecifiedChain(String pdbId,
 229           String searchTerm)
 230   {
 231     String pdbIdWithChainCode = "";
 232     if (searchTerm.contains(";"))
 233     {
 234       String[] foundTerms = searchTerm.split(";");
 235       for (String foundTerm : foundTerms)
 236       {
 237         if (foundTerm.contains(pdbId))
 238         {
 239           pdbIdWithChainCode = foundTerm;
 240         }
 241       }
 242     }
 243     else if (searchTerm.contains(pdbId))
 244     {
 245       pdbIdWithChainCode = searchTerm;
 246     }
 247     else
 248     {
 249       pdbIdWithChainCode = pdbId;
 250     }
 251     return pdbIdWithChainCode;
 252   }
 253
 254   @Override
 255   public FTSRestClientI getFTSRestClient()
 256   {
 257     return PDBFTSRestClient.getInstance();
 258   }
 259
 260   @Override
 261   public String getFTSFrameTitle()
 262   {
 263     return defaultFTSFrameTitle;
 264   }
 265
 266   @Override
 267   public boolean isPaginationEnabled()
 268   {
 269     return true;
 270   }
 271
 272   @Override
 273   public Map<String, Integer> getTempUserPrefs()
 274   {
 275     return tempUserPrefs;
 276   }
 277
 278   @Override
 279   public String getCacheKey()
 280   {
 281     return PDB_FTS_CACHE_KEY;
 282   }
 283
 284 }