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().size();
 111           String result = (resultSetCount > 0) ? MessageManager
 112                   .getString("label.results") : MessageManager
 113                   .getString("label.result");
 114
 115           if (isPaginationEnabled() && resultSetCount > 0)
 116           {
 117             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 118                     + " " + (offSet + 1) + " to "
 119                     + (offSet + resultSetCount) + " of "
 120                     + totalResultSetCount
 121                     + " " + " (" + (endTime - startTime) + " milli secs)");
 122           }
 123           else
 124           {
 125             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 126                     + resultSetCount + " " + result + " ("
 127                     + (endTime - startTime) + " milli secs)");
 128           }
 129
 130           setSearchInProgress(false);
 131           refreshPaginatorState();
 132         }
 133       }
 134     }.start();
 135   }
 136
 137   public static String decodeSearchTerm(String enteredText,
 138           String targetField)
 139   {
 140     String foundSearchTerms = enteredText;
 141     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 142     if (enteredText.contains(";"))
 143     {
 144       String[] searchTerms = enteredText.split(";");
 145       for (String searchTerm : searchTerms)
 146       {
 147         if (searchTerm.contains(":"))
 148         {
 149           foundSearchTermsBuilder.append(targetField).append(":")
 150                   .append(searchTerm.split(":")[0]).append(" OR ");
 151         }
 152         else
 153         {
 154           foundSearchTermsBuilder.append(targetField).append(":")
 155                   .append(searchTerm).append(" OR ");
 156         }
 157       }
 158       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 159       foundSearchTerms = foundSearchTermsBuilder.toString();
 160       if (foundSearchTerms.contains(" OR "))
 161       {
 162         foundSearchTerms = foundSearchTerms.substring(
 163                 targetField.length() + 1, endIndex);
 164       }
 165     }
 166     else if (enteredText.contains(":"))
 167     {
 168       foundSearchTerms = foundSearchTerms.split(":")[0];
 169     }
 170     return foundSearchTerms;
 171   }
 172
 173   @Override
 174   public void okAction()
 175   {
 176     // mainFrame.dispose();
 177     disableActionButtons();
 178     StringBuilder selectedIds = new StringBuilder();
 179     HashSet<String> selectedIdsSet = new HashSet<String>();
 180     int primaryKeyColIndex = 0;
 181     try
 182     {
 183       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 184               wantedFields,
 185               false);
 186     } catch (Exception e)
 187     {
 188       e.printStackTrace();
 189     }
 190     int[] selectedRows = getResultTable().getSelectedRows();
 191     for (int summaryRow : selectedRows)
 192     {
 193       String idStr = getResultTable().getValueAt(summaryRow,
 194               primaryKeyColIndex)
 195               .toString();
 196       String searchTerm = txt_search.getText();
 197       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 198     }
 199
 200     for (String selectedId : selectedIdsSet)
 201     {
 202       selectedIds.append(selectedId).append(";");
 203     }
 204
 205     String ids = selectedIds.toString();
 206     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 207     seqFetcher.getTextArea().setText(ids);
 208     Thread worker = new Thread(seqFetcher);
 209     worker.start();
 210     delayAndEnableActionButtons();
 211   }
 212
 213
 214   public static String getPDBIdwithSpecifiedChain(String pdbId,
 215           String searchTerm)
 216   {
 217     String pdbIdWithChainCode = "";
 218     if (searchTerm.contains(";"))
 219     {
 220       String[] foundTerms = searchTerm.split(";");
 221       for (String foundTerm : foundTerms)
 222       {
 223         if (foundTerm.contains(pdbId))
 224         {
 225           pdbIdWithChainCode = foundTerm;
 226         }
 227       }
 228     }
 229     else if (searchTerm.contains(pdbId))
 230     {
 231       pdbIdWithChainCode = searchTerm;
 232     }
 233     else
 234     {
 235       pdbIdWithChainCode = pdbId;
 236     }
 237     return pdbIdWithChainCode;
 238   }
 239
 240   @Override
 241   public FTSRestClientI getFTSRestClient()
 242   {
 243     return PDBFTSRestClient.getInstance();
 244   }
 245
 246   @Override
 247   public String getFTSFrameTitle()
 248   {
 249     return ftsFrameTitle;
 250   }
 251
 252   @Override
 253   public boolean isPaginationEnabled()
 254   {
 255     return true;
 256   }
 257
 258 }