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