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
  43   private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
  44
  45   private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
  46
  47   public PDBFTSPanel(SequenceFetcher seqFetcher)
  48   {
  49     super();
  50     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
  51     this.seqFetcher = seqFetcher;
  52     this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
  53             .getProgressIndicator();
  54   }
  55
  56   @Override
  57   public void searchAction(boolean isFreshSearch)
  58   {
  59     mainFrame.requestFocusInWindow();
  60     if (isFreshSearch)
  61     {
  62       offSet = 0;
  63     }
  64     new Thread()
  65     {
  66       @Override
  67       public void run()
  68       {
  69         reset();
  70         boolean allowEmptySequence = false;
  71         if (getTypedText().length() > 0)
  72         {
  73           setSearchInProgress(true);
  74           long startTime = System.currentTimeMillis();
  75
  76           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  77                   .getSelectedItem()).getCode();
  78           wantedFields = PDBFTSRestClient.getInstance()
  79                   .getAllDefaultDisplayedFTSDataColumns();
  80           String searchTerm = decodeSearchTerm(getTypedText(),
  81                   searchTarget);
  82
  83           FTSRestRequest request = new FTSRestRequest();
  84           request.setAllowEmptySeq(allowEmptySequence);
  85           request.setResponseSize(100);
  86           request.setFieldToSearchBy("(" + searchTarget + ":");
  87           request.setSearchTerm(searchTerm + ")");
  88           request.setOffSet(offSet);
  89           request.setWantedFields(wantedFields);
  90           FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
  91           FTSRestResponse resultList;
  92           try
  93           {
  94             resultList = pdbRestCleint.executeRequest(request);
  95           } catch (Exception e)
  96           {
  97             setErrorMessage(e.getMessage());
  98             checkForErrors();
  99             return;
 100           }
 101
 102           if (resultList.getSearchSummary() != null
 103                   && resultList.getSearchSummary().size() > 0)
 104           {
 105             getResultTable().setModel(
 106                     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) ? MessageManager
 118                   .getString("label.results") : MessageManager
 119                   .getString("label.result");
 120
 121           if (isPaginationEnabled() && resultSetCount > 0)
 122           {
 123             updateSearchFrameTitle(defaultFTSFrameTitle
 124                     + " - "
 125                     + result
 126                     + " "
 127                     + totalNumberformatter.format((Number) (offSet + 1))
 128                     + " to "
 129                     + totalNumberformatter
 130                             .format((Number) (offSet + resultSetCount))
 131                     + " of "
 132                     + totalNumberformatter
 133                             .format((Number) totalResultSetCount) + " "
 134                     + " (" + (endTime - startTime) + " milli secs)");
 135           }
 136           else
 137           {
 138             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 139                     + resultSetCount + " " + result + " ("
 140                     + (endTime - startTime) + " milli secs)");
 141           }
 142
 143           setSearchInProgress(false);
 144           refreshPaginatorState();
 145           updateSummaryTableSelections();
 146         }
 147         txt_search.updateCache();
 148       }
 149     }.start();
 150   }
 151
 152   public static String decodeSearchTerm(String enteredText,
 153           String targetField)
 154   {
 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         if (searchTerm.contains(":"))
 163         {
 164           foundSearchTermsBuilder.append(targetField).append(":")
 165                   .append(searchTerm.split(":")[0]).append(" OR ");
 166         }
 167         else
 168         {
 169           foundSearchTermsBuilder.append(targetField).append(":")
 170                   .append(searchTerm).append(" OR ");
 171         }
 172       }
 173       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 174       foundSearchTerms = foundSearchTermsBuilder.toString();
 175       if (foundSearchTerms.contains(" OR "))
 176       {
 177         foundSearchTerms = foundSearchTerms.substring(
 178                 targetField.length() + 1, endIndex);
 179       }
 180     }
 181     else if (enteredText.contains(":"))
 182     {
 183       foundSearchTerms = foundSearchTerms.split(":")[0];
 184     }
 185     return foundSearchTerms;
 186   }
 187
 188   @Override
 189   public void okAction()
 190   {
 191     // mainFrame.dispose();
 192     disableActionButtons();
 193     StringBuilder selectedIds = new StringBuilder();
 194     HashSet<String> selectedIdsSet = new HashSet<String>();
 195     int primaryKeyColIndex = 0;
 196     try
 197     {
 198       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 199               wantedFields, false);
 200     } catch (Exception e)
 201     {
 202       e.printStackTrace();
 203     }
 204     int[] selectedRows = getResultTable().getSelectedRows();
 205     String searchTerm = getTypedText();
 206     for (int summaryRow : selectedRows)
 207     {
 208       String idStr = getResultTable().getValueAt(summaryRow,
 209               primaryKeyColIndex).toString();
 210       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 211     }
 212
 213     for (String idStr : paginatorCart)
 214     {
 215       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 216     }
 217
 218     for (String selectedId : selectedIdsSet)
 219     {
 220       selectedIds.append(selectedId).append(";");
 221     }
 222
 223     String ids = selectedIds.toString();
 224     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 225     seqFetcher.getTextArea().setText(ids);
 226     Thread worker = new Thread(seqFetcher);
 227     worker.start();
 228     delayAndEnableActionButtons();
 229   }
 230
 231   public static String getPDBIdwithSpecifiedChain(String pdbId,
 232           String searchTerm)
 233   {
 234     String pdbIdWithChainCode = "";
 235     if (searchTerm.contains(";"))
 236     {
 237       String[] foundTerms = searchTerm.split(";");
 238       for (String foundTerm : foundTerms)
 239       {
 240         if (foundTerm.contains(pdbId))
 241         {
 242           pdbIdWithChainCode = foundTerm;
 243         }
 244       }
 245     }
 246     else if (searchTerm.contains(pdbId))
 247     {
 248       pdbIdWithChainCode = searchTerm;
 249     }
 250     else
 251     {
 252       pdbIdWithChainCode = pdbId;
 253     }
 254     return pdbIdWithChainCode;
 255   }
 256
 257   @Override
 258   public FTSRestClientI getFTSRestClient()
 259   {
 260     return PDBFTSRestClient.getInstance();
 261   }
 262
 263   @Override
 264   public String getFTSFrameTitle()
 265   {
 266     return defaultFTSFrameTitle;
 267   }
 268
 269   @Override
 270   public boolean isPaginationEnabled()
 271   {
 272     return true;
 273   }
 274
 275   @Override
 276   public Map<String, Integer> getTempUserPrefs()
 277   {
 278     return tempUserPrefs;
 279   }
 280
 281
 282   @Override
 283   public String getCacheKey()
 284   {
 285     return PDB_FTS_CACHE_KEY;
 286   }
 287
 288
 289 }