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.Help;
  30 import jalview.gui.Help.HelpId;
  31 import jalview.gui.SequenceFetcher;
  32 import jalview.util.MessageManager;
  33
  34 import java.util.HashMap;
  35 import java.util.HashSet;
  36 import java.util.Map;
  37
  38 import javax.help.HelpSetException;
  39
  40 @SuppressWarnings("serial")
  41 public class PDBFTSPanel extends GFTSPanel
  42 {
  43   private static String defaultFTSFrameTitle = MessageManager
  44           .getString("label.pdb_sequence_fetcher");
  45
  46   private static Map<String, Integer> tempUserPrefs = new HashMap<>();
  47
  48   private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
  49
  50   private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH";
  51
  52   public PDBFTSPanel(SequenceFetcher fetcher)
  53   {
  54     super(fetcher);
  55     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
  56     this.seqFetcher = fetcher;
  57     this.progressIndicator = (fetcher == null) ? null
  58             : fetcher.getProgressIndicator();
  59   }
  60
  61   @Override
  62   public void searchAction(boolean isFreshSearch)
  63   {
  64     mainFrame.requestFocusInWindow();
  65     if (isFreshSearch)
  66     {
  67       offSet = 0;
  68     }
  69     new Thread()
  70     {
  71       @Override
  72       public void run()
  73       {
  74         reset();
  75         boolean allowEmptySequence = false;
  76         if (getTypedText().length() > 0)
  77         {
  78           setSearchInProgress(true);
  79           long startTime = System.currentTimeMillis();
  80
  81           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  82                   .getSelectedItem()).getCode();
  83           wantedFields = PDBFTSRestClient.getInstance()
  84                   .getAllDefaultDisplayedFTSDataColumns();
  85           String searchTerm = decodeSearchTerm(getTypedText(),
  86                   searchTarget);
  87
  88           FTSRestRequest request = new FTSRestRequest();
  89           request.setAllowEmptySeq(allowEmptySequence);
  90           request.setResponseSize(100);
  91           request.setFieldToSearchBy("(" + searchTarget + ":");
  92           request.setSearchTerm(searchTerm + ")");
  93           request.setOffSet(offSet);
  94           request.setWantedFields(wantedFields);
  95           FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
  96           FTSRestResponse resultList;
  97           try
  98           {
  99             resultList = pdbRestClient.executeRequest(request);
 100           } catch (Exception e)
 101           {
 102             setErrorMessage(e.getMessage());
 103             checkForErrors();
 104             setSearchInProgress(false);
 105             return;
 106           }
 107
 108           if (resultList.getSearchSummary() != null
 109                   && resultList.getSearchSummary().size() > 0)
 110           {
 111             getResultTable().setModel(FTSRestResponse.getTableModel(request,
 112                     resultList.getSearchSummary()));
 113             FTSRestResponse.configureTableColumn(getResultTable(),
 114                     wantedFields, tempUserPrefs);
 115             getResultTable().setVisible(true);
 116           }
 117
 118           long endTime = System.currentTimeMillis();
 119           totalResultSetCount = resultList.getNumberOfItemsFound();
 120           resultSetCount = resultList.getSearchSummary() == null ? 0
 121                   : resultList.getSearchSummary().size();
 122           String result = (resultSetCount > 0)
 123                   ? MessageManager.getString("label.results")
 124                   : MessageManager.getString("label.result");
 125
 126           if (isPaginationEnabled() && resultSetCount > 0)
 127           {
 128             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 129                     + " "
 130                     + totalNumberformatter.format((Number) (offSet + 1))
 131                     + " to "
 132                     + totalNumberformatter
 133                             .format((Number) (offSet + resultSetCount))
 134                     + " of "
 135                     + totalNumberformatter
 136                             .format((Number) totalResultSetCount)
 137                     + " " + " (" + (endTime - startTime) + " milli secs)");
 138           }
 139           else
 140           {
 141             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 142                     + resultSetCount + " " + result + " ("
 143                     + (endTime - startTime) + " milli secs)");
 144           }
 145
 146           setSearchInProgress(false);
 147           refreshPaginatorState();
 148           updateSummaryTableSelections();
 149         }
 150         txt_search.updateCache();
 151       }
 152     }.start();
 153   }
 154
 155   public static String decodeSearchTerm(String enteredText,
 156           String targetField)
 157   {
 158     String foundSearchTerms = enteredText;
 159     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 160     if (enteredText.contains(";"))
 161     {
 162       String[] searchTerms = enteredText.split(";");
 163       for (String searchTerm : searchTerms)
 164       {
 165         if (searchTerm.contains(":"))
 166         {
 167           foundSearchTermsBuilder.append(targetField).append(":")
 168                   .append(searchTerm.split(":")[0]).append(" OR ");
 169         }
 170         else
 171         {
 172           foundSearchTermsBuilder.append(targetField).append(":")
 173                   .append(searchTerm).append(" OR ");
 174         }
 175       }
 176       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 177       foundSearchTerms = foundSearchTermsBuilder.toString();
 178       if (foundSearchTerms.contains(" OR "))
 179       {
 180         foundSearchTerms = foundSearchTerms
 181                 .substring(targetField.length() + 1, endIndex);
 182       }
 183     }
 184     else if (enteredText.contains(":"))
 185     {
 186       foundSearchTerms = foundSearchTerms.split(":")[0];
 187     }
 188     return foundSearchTerms;
 189   }
 190
 191   @Override
 192   public void okAction()
 193   {
 194     // mainFrame.dispose();
 195     disableActionButtons();
 196     StringBuilder selectedIds = new StringBuilder();
 197     HashSet<String> selectedIdsSet = new HashSet<>();
 198     int primaryKeyColIndex = 0;
 199     try
 200     {
 201       primaryKeyColIndex = getFTSRestClient()
 202               .getPrimaryKeyColumIndex(wantedFields, false);
 203     } catch (Exception e)
 204     {
 205       e.printStackTrace();
 206     }
 207     int[] selectedRows = getResultTable().getSelectedRows();
 208     String searchTerm = getTypedText();
 209     for (int summaryRow : selectedRows)
 210     {
 211       String idStr = getResultTable()
 212               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 213       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 214     }
 215
 216     for (String idStr : paginatorCart)
 217     {
 218       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 219     }
 220
 221     for (String selectedId : selectedIdsSet)
 222     {
 223       selectedIds.append(selectedId).append(";");
 224     }
 225
 226     String ids = selectedIds.toString();
 227     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 228     seqFetcher.getTextArea().setText(ids);
 229     Thread worker = new Thread(seqFetcher);
 230     worker.start();
 231     delayAndEnableActionButtons();
 232   }
 233
 234   public static String getPDBIdwithSpecifiedChain(String pdbId,
 235           String searchTerm)
 236   {
 237     String pdbIdWithChainCode = "";
 238     if (searchTerm.contains(";"))
 239     {
 240       String[] foundTerms = searchTerm.split(";");
 241       for (String foundTerm : foundTerms)
 242       {
 243         if (foundTerm.contains(pdbId))
 244         {
 245           pdbIdWithChainCode = foundTerm;
 246         }
 247       }
 248     }
 249     else if (searchTerm.contains(pdbId))
 250     {
 251       pdbIdWithChainCode = searchTerm;
 252     }
 253     else
 254     {
 255       pdbIdWithChainCode = pdbId;
 256     }
 257     return pdbIdWithChainCode;
 258   }
 259
 260   @Override
 261   public FTSRestClientI getFTSRestClient()
 262   {
 263     return PDBFTSRestClient.getInstance();
 264   }
 265
 266   @Override
 267   public String getFTSFrameTitle()
 268   {
 269     return defaultFTSFrameTitle;
 270   }
 271
 272   @Override
 273   public boolean isPaginationEnabled()
 274   {
 275     return true;
 276   }
 277
 278   @Override
 279   public Map<String, Integer> getTempUserPrefs()
 280   {
 281     return tempUserPrefs;
 282   }
 283
 284   @Override
 285   public String getCacheKey()
 286   {
 287     return PDB_FTS_CACHE_KEY;
 288   }
 289
 290   @Override
 291   public String getAutosearchPreference()
 292   {
 293     return PDB_AUTOSEARCH;
 294   }
 295
 296   @Override
 297   protected void showHelp()
 298   {
 299     try
 300     {
 301       Help.showHelpWindow(HelpId.PdbFts);
 302     } catch (HelpSetException e1)
 303     {
 304       e1.printStackTrace();
 305     }
 306  }
 307 }