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     pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
  49     this.seqFetcher = seqFetcher;
  50     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  51             .getProgressIndicator();
  52   }
  53
  54
  55   @Override
  56   public void searchAction(boolean isFreshSearch)
  57   {
  58     if (isFreshSearch)
  59     {
  60       offSet = 0;
  61     }
  62     new Thread()
  63     {
  64       @Override
  65       public void run()
  66       {
  67         ftsFrameTitle = defaultFTSFrameTitle;
  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(txt_search.getText(),
  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 pdbRestCleint = PDBFTSRestClient.getInstance();
  90           FTSRestResponse resultList;
  91           try
  92           {
  93             resultList = pdbRestCleint.executeRequest(request);
  94           } catch (Exception e)
  95           {
  96             setErrorMessage(e.getMessage());
  97             checkForErrors();
  98             return;
  99           }
 100
 101           if (resultList.getSearchSummary() != null
 102                   && resultList.getSearchSummary().size() > 0)
 103           {
 104             getResultTable().setModel(
 105                     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) ? MessageManager
 117                   .getString("label.results") : MessageManager
 118                   .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       }
 145     }.start();
 146   }
 147
 148   public static String decodeSearchTerm(String enteredText,
 149           String targetField)
 150   {
 151     String foundSearchTerms = enteredText;
 152     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 153     if (enteredText.contains(";"))
 154     {
 155       String[] searchTerms = enteredText.split(";");
 156       for (String searchTerm : searchTerms)
 157       {
 158         if (searchTerm.contains(":"))
 159         {
 160           foundSearchTermsBuilder.append(targetField).append(":")
 161                   .append(searchTerm.split(":")[0]).append(" OR ");
 162         }
 163         else
 164         {
 165           foundSearchTermsBuilder.append(targetField).append(":")
 166                   .append(searchTerm).append(" OR ");
 167         }
 168       }
 169       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 170       foundSearchTerms = foundSearchTermsBuilder.toString();
 171       if (foundSearchTerms.contains(" OR "))
 172       {
 173         foundSearchTerms = foundSearchTerms.substring(
 174                 targetField.length() + 1, endIndex);
 175       }
 176     }
 177     else if (enteredText.contains(":"))
 178     {
 179       foundSearchTerms = foundSearchTerms.split(":")[0];
 180     }
 181     return foundSearchTerms;
 182   }
 183
 184   @Override
 185   public void okAction()
 186   {
 187     // mainFrame.dispose();
 188     disableActionButtons();
 189     StringBuilder selectedIds = new StringBuilder();
 190     HashSet<String> selectedIdsSet = new HashSet<String>();
 191     int primaryKeyColIndex = 0;
 192     try
 193     {
 194       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 195               wantedFields,
 196               false);
 197     } catch (Exception e)
 198     {
 199       e.printStackTrace();
 200     }
 201     int[] selectedRows = getResultTable().getSelectedRows();
 202     String searchTerm = txt_search.getText();
 203     for (int summaryRow : selectedRows)
 204     {
 205       String idStr = getResultTable().getValueAt(summaryRow,
 206               primaryKeyColIndex)
 207               .toString();
 208       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 209     }
 210
 211     for (String idStr : paginatorCart)
 212     {
 213       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 214     }
 215
 216     for (String selectedId : selectedIdsSet)
 217     {
 218       selectedIds.append(selectedId).append(";");
 219     }
 220
 221     String ids = selectedIds.toString();
 222     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 223     seqFetcher.getTextArea().setText(ids);
 224     Thread worker = new Thread(seqFetcher);
 225     worker.start();
 226     delayAndEnableActionButtons();
 227   }
 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 ftsFrameTitle;
 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 }