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   @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
 123                     + " - "
 124                     + 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       }
 147     }.start();
 148   }
 149
 150   public static String decodeSearchTerm(String enteredText,
 151           String targetField)
 152   {
 153     String foundSearchTerms = enteredText;
 154     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 155     if (enteredText.contains(";"))
 156     {
 157       String[] searchTerms = enteredText.split(";");
 158       for (String searchTerm : searchTerms)
 159       {
 160         if (searchTerm.contains(":"))
 161         {
 162           foundSearchTermsBuilder.append(targetField).append(":")
 163                   .append(searchTerm.split(":")[0]).append(" OR ");
 164         }
 165         else
 166         {
 167           foundSearchTermsBuilder.append(targetField).append(":")
 168                   .append(searchTerm).append(" OR ");
 169         }
 170       }
 171       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 172       foundSearchTerms = foundSearchTermsBuilder.toString();
 173       if (foundSearchTerms.contains(" OR "))
 174       {
 175         foundSearchTerms = foundSearchTerms.substring(
 176                 targetField.length() + 1, endIndex);
 177       }
 178     }
 179     else if (enteredText.contains(":"))
 180     {
 181       foundSearchTerms = foundSearchTerms.split(":")[0];
 182     }
 183     return foundSearchTerms;
 184   }
 185
 186   @Override
 187   public void okAction()
 188   {
 189     // mainFrame.dispose();
 190     disableActionButtons();
 191     StringBuilder selectedIds = new StringBuilder();
 192     HashSet<String> selectedIdsSet = new HashSet<String>();
 193     int primaryKeyColIndex = 0;
 194     try
 195     {
 196       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 197               wantedFields, 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).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   public static String getPDBIdwithSpecifiedChain(String pdbId,
 230           String searchTerm)
 231   {
 232     String pdbIdWithChainCode = "";
 233     if (searchTerm.contains(";"))
 234     {
 235       String[] foundTerms = searchTerm.split(";");
 236       for (String foundTerm : foundTerms)
 237       {
 238         if (foundTerm.contains(pdbId))
 239         {
 240           pdbIdWithChainCode = foundTerm;
 241         }
 242       }
 243     }
 244     else if (searchTerm.contains(pdbId))
 245     {
 246       pdbIdWithChainCode = searchTerm;
 247     }
 248     else
 249     {
 250       pdbIdWithChainCode = pdbId;
 251     }
 252     return pdbIdWithChainCode;
 253   }
 254
 255   @Override
 256   public FTSRestClientI getFTSRestClient()
 257   {
 258     return PDBFTSRestClient.getInstance();
 259   }
 260
 261   @Override
 262   public String getFTSFrameTitle()
 263   {
 264     return ftsFrameTitle;
 265   }
 266
 267   @Override
 268   public boolean isPaginationEnabled()
 269   {
 270     return true;
 271   }
 272
 273   @Override
 274   public Map<String, Integer> getTempUserPrefs()
 275   {
 276     return tempUserPrefs;
 277   }
 278
 279 }