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