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                     + " " + (offSet + 1) + " to "
 120                     + (offSet + resultSetCount) + " of "
 121                     + totalResultSetCount
 122                     + " " + " (" + (endTime - startTime) + " milli secs)");
 123           }
 124           else
 125           {
 126             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 127                     + resultSetCount + " " + result + " ("
 128                     + (endTime - startTime) + " milli secs)");
 129           }
 130
 131           setSearchInProgress(false);
 132           refreshPaginatorState();
 133           updateSummaryTableSelections();
 134         }
 135       }
 136     }.start();
 137   }
 138
 139   public static String decodeSearchTerm(String enteredText,
 140           String targetField)
 141   {
 142     String foundSearchTerms = enteredText;
 143     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 144     if (enteredText.contains(";"))
 145     {
 146       String[] searchTerms = enteredText.split(";");
 147       for (String searchTerm : searchTerms)
 148       {
 149         if (searchTerm.contains(":"))
 150         {
 151           foundSearchTermsBuilder.append(targetField).append(":")
 152                   .append(searchTerm.split(":")[0]).append(" OR ");
 153         }
 154         else
 155         {
 156           foundSearchTermsBuilder.append(targetField).append(":")
 157                   .append(searchTerm).append(" OR ");
 158         }
 159       }
 160       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 161       foundSearchTerms = foundSearchTermsBuilder.toString();
 162       if (foundSearchTerms.contains(" OR "))
 163       {
 164         foundSearchTerms = foundSearchTerms.substring(
 165                 targetField.length() + 1, endIndex);
 166       }
 167     }
 168     else if (enteredText.contains(":"))
 169     {
 170       foundSearchTerms = foundSearchTerms.split(":")[0];
 171     }
 172     return foundSearchTerms;
 173   }
 174
 175   @Override
 176   public void okAction()
 177   {
 178     // mainFrame.dispose();
 179     disableActionButtons();
 180     StringBuilder selectedIds = new StringBuilder();
 181     HashSet<String> selectedIdsSet = new HashSet<String>();
 182     int primaryKeyColIndex = 0;
 183     try
 184     {
 185       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 186               wantedFields,
 187               false);
 188     } catch (Exception e)
 189     {
 190       e.printStackTrace();
 191     }
 192     int[] selectedRows = getResultTable().getSelectedRows();
 193     String searchTerm = txt_search.getText();
 194     for (int summaryRow : selectedRows)
 195     {
 196       String idStr = getResultTable().getValueAt(summaryRow,
 197               primaryKeyColIndex)
 198               .toString();
 199       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 200     }
 201
 202     for (String idStr : paginatorCart)
 203     {
 204       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 205     }
 206
 207     for (String selectedId : selectedIdsSet)
 208     {
 209       selectedIds.append(selectedId).append(";");
 210     }
 211
 212     String ids = selectedIds.toString();
 213     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 214     seqFetcher.getTextArea().setText(ids);
 215     Thread worker = new Thread(seqFetcher);
 216     worker.start();
 217     delayAndEnableActionButtons();
 218   }
 219
 220
 221   public static String getPDBIdwithSpecifiedChain(String pdbId,
 222           String searchTerm)
 223   {
 224     String pdbIdWithChainCode = "";
 225     if (searchTerm.contains(";"))
 226     {
 227       String[] foundTerms = searchTerm.split(";");
 228       for (String foundTerm : foundTerms)
 229       {
 230         if (foundTerm.contains(pdbId))
 231         {
 232           pdbIdWithChainCode = foundTerm;
 233         }
 234       }
 235     }
 236     else if (searchTerm.contains(pdbId))
 237     {
 238       pdbIdWithChainCode = searchTerm;
 239     }
 240     else
 241     {
 242       pdbIdWithChainCode = pdbId;
 243     }
 244     return pdbIdWithChainCode;
 245   }
 246
 247   @Override
 248   public FTSRestClientI getFTSRestClient()
 249   {
 250     return PDBFTSRestClient.getInstance();
 251   }
 252
 253   @Override
 254   public String getFTSFrameTitle()
 255   {
 256     return ftsFrameTitle;
 257   }
 258
 259   @Override
 260   public boolean isPaginationEnabled()
 261   {
 262     return true;
 263   }
 264
 265 }