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 String ftsFrameTitle = defaultFTSFrameTitle;
  43
  44   private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
  45
  46   public PDBFTSPanel(SequenceFetcher seqFetcher)
  47   {
  48     super();
  49     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
  50     this.seqFetcher = seqFetcher;
  51     this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
  52             .getProgressIndicator();
  53   }
  54
  55
  56   @Override
  57   public void searchAction(boolean isFreshSearch)
  58   {
  59     if (isFreshSearch)
  60     {
  61       offSet = 0;
  62     }
  63     new Thread()
  64     {
  65       @Override
  66       public void run()
  67       {
  68         ftsFrameTitle = defaultFTSFrameTitle;
  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(txt_search.getText(),
  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 + " - " + result
 124                     + " "
 125                     + totalNumberformatter.format((Number) (offSet + 1))
 126                     + " to "
 127                     + totalNumberformatter
 128                             .format((Number) (offSet + resultSetCount))
 129                     + " of "
 130                     + totalNumberformatter
 131                             .format((Number) totalResultSetCount)
 132                     + " " + " (" + (endTime - startTime) + " milli secs)");
 133           }
 134           else
 135           {
 136             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 137                     + resultSetCount + " " + result + " ("
 138                     + (endTime - startTime) + " milli secs)");
 139           }
 140
 141           setSearchInProgress(false);
 142           refreshPaginatorState();
 143           updateSummaryTableSelections();
 144         }
 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.substring(
 175                 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().getPrimaryKeyColumIndex(
 196               wantedFields,
 197               false);
 198     } catch (Exception e)
 199     {
 200       e.printStackTrace();
 201     }
 202     int[] selectedRows = getResultTable().getSelectedRows();
 203     String searchTerm = txt_search.getText();
 204     for (int summaryRow : selectedRows)
 205     {
 206       String idStr = getResultTable().getValueAt(summaryRow,
 207               primaryKeyColIndex)
 208               .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);
 226     worker.start();
 227     delayAndEnableActionButtons();
 228   }
 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 ftsFrameTitle;
 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 }