src/jalview/fts/service/uniprot/UniprotFTSPanel.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.uniprot;
  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.Help;
  30 import jalview.gui.Help.HelpId;
  31 import jalview.gui.SequenceFetcher;
  32 import jalview.util.MessageManager;
  33
  34 import java.util.HashMap;
  35 import java.util.HashSet;
  36 import java.util.Map;
  37
  38 import javax.help.HelpSetException;
  39
  40 @SuppressWarnings("serial")
  41 public class UniprotFTSPanel extends GFTSPanel
  42 {
  43
  44   private static String defaultFTSFrameTitle = MessageManager
  45           .getString("label.uniprot_sequence_fetcher");
  46
  47   private static Map<String, Integer> tempUserPrefs = new HashMap<>();
  48
  49   private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
  50
  51   private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
  52
  53   public UniprotFTSPanel(SequenceFetcher fetcher)
  54   {
  55     super(fetcher);
  56     pageLimit = UniProtFTSRestClient.getInstance()
  57             .getDefaultResponsePageSize();
  58     this.seqFetcher = fetcher;
  59     this.progressIndicator = (fetcher == null) ? null
  60             : fetcher.getProgressIndicator();
  61   }
  62
  63   @Override
  64   public void searchAction(boolean isFreshSearch)
  65   {
  66     mainFrame.requestFocusInWindow();
  67     if (isFreshSearch)
  68     {
  69       offSet = 0;
  70     }
  71     new Thread()
  72     {
  73       @Override
  74       public void run()
  75       {
  76         reset();
  77         String searchInput = getTypedText();
  78         if (searchInput.length() > 0)
  79         {
  80           setSearchInProgress(true);
  81           long startTime = System.currentTimeMillis();
  82           searchInput = getTypedText();
  83           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  84                   .getSelectedItem()).getAltCode();
  85           wantedFields = UniProtFTSRestClient.getInstance()
  86                   .getAllDefaultDisplayedFTSDataColumns();
  87           String searchTerm = decodeSearchTerm(searchInput, searchTarget);
  88
  89           FTSRestRequest request = new FTSRestRequest();
  90           request.setFieldToSearchBy(searchTarget);
  91           request.setSearchTerm(searchTerm);
  92           request.setOffSet(offSet);
  93           request.setWantedFields(wantedFields);
  94           FTSRestClientI uniProtRestClient = UniProtFTSRestClient
  95                   .getInstance();
  96           FTSRestResponse resultList;
  97           try
  98           {
  99             resultList = uniProtRestClient.executeRequest(request);
 100           } catch (Exception e)
 101           {
 102             setErrorMessage(e.getMessage());
 103             checkForErrors();
 104             setSearchInProgress(false);
 105             return;
 106           }
 107
 108           if (resultList.getSearchSummary() != null
 109                   && resultList.getSearchSummary().size() > 0)
 110           {
 111             getResultTable().setModel(FTSRestResponse.getTableModel(request,
 112                     resultList.getSearchSummary()));
 113             FTSRestResponse.configureTableColumn(getResultTable(),
 114                     wantedFields, tempUserPrefs);
 115             getResultTable().setVisible(true);
 116           }
 117
 118           long endTime = System.currentTimeMillis();
 119           totalResultSetCount = resultList.getNumberOfItemsFound();
 120           resultSetCount = resultList.getSearchSummary() == null ? 0
 121                   : resultList.getSearchSummary().size();
 122           String result = (resultSetCount > 0)
 123                   ? MessageManager.getString("label.results")
 124                   : MessageManager.getString("label.result");
 125           if (isPaginationEnabled() && resultSetCount > 0)
 126           {
 127             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 128                     + " "
 129                     + totalNumberformatter.format((Number) (offSet + 1))
 130                     + " to "
 131                     + totalNumberformatter
 132                             .format((Number) (offSet + resultSetCount))
 133                     + " of "
 134                     + totalNumberformatter
 135                             .format((Number) totalResultSetCount)
 136                     + " " + " (" + (endTime - startTime) + " milli secs)");
 137           }
 138           else
 139           {
 140             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 141                     + resultSetCount + " " + result + " ("
 142                     + (endTime - startTime) + " milli secs)");
 143           }
 144           setSearchInProgress(false);
 145           refreshPaginatorState();
 146           updateSummaryTableSelections();
 147         }
 148         txt_search.updateCache();
 149       }
 150     }.start();
 151
 152   }
 153
 154   public String decodeSearchTerm(String enteredText, String targetField)
 155   {
 156     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 157             : targetField.length() + 1;
 158     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 159             : targetField + ":";
 160     String foundSearchTerms = enteredText;
 161     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 162     if (enteredText.contains(";"))
 163     {
 164       String[] searchTerms = enteredText.split(";");
 165       for (String searchTerm : searchTerms)
 166       {
 167         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 168                 .append(" OR ");
 169       }
 170       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 171       foundSearchTerms = foundSearchTermsBuilder.toString();
 172       if (foundSearchTerms.contains(" OR "))
 173       {
 174         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 175                 endIndex);
 176       }
 177     }
 178     return foundSearchTerms;
 179   }
 180
 181   @Override
 182   public boolean isPaginationEnabled()
 183   {
 184     return true;
 185   }
 186
 187   @Override
 188   public void okAction()
 189   {
 190     disableActionButtons();
 191     StringBuilder selectedIds = new StringBuilder();
 192     HashSet<String> selectedIdsSet = new HashSet<>();
 193     int primaryKeyColIndex = 0;
 194     try
 195     {
 196       primaryKeyColIndex = getFTSRestClient()
 197               .getPrimaryKeyColumIndex(wantedFields, false);
 198     } catch (Exception e)
 199     {
 200       e.printStackTrace();
 201     }
 202     int[] selectedRows = getResultTable().getSelectedRows();
 203     for (int summaryRow : selectedRows)
 204     {
 205       String idStr = getResultTable()
 206               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 207       selectedIdsSet.add(idStr);
 208     }
 209     selectedIdsSet.addAll(paginatorCart);
 210     for (String selectedId : selectedIdsSet)
 211     {
 212       selectedIds.append(selectedId).append(";");
 213     }
 214
 215     String ids = selectedIds.toString();
 216     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 217     seqFetcher.getTextArea().setText(ids);
 218     Thread worker = new Thread(seqFetcher);
 219     worker.start();
 220     delayAndEnableActionButtons();
 221   }
 222
 223   @Override
 224   public FTSRestClientI getFTSRestClient()
 225   {
 226     return UniProtFTSRestClient.getInstance();
 227   }
 228
 229   @Override
 230   public String getFTSFrameTitle()
 231   {
 232     return defaultFTSFrameTitle;
 233   }
 234
 235   @Override
 236   public Map<String, Integer> getTempUserPrefs()
 237   {
 238     return tempUserPrefs;
 239   }
 240
 241   @Override
 242   public String getCacheKey()
 243   {
 244     return UNIPROT_FTS_CACHE_KEY;
 245   }
 246
 247   @Override
 248   public String getAutosearchPreference()
 249   {
 250     return UNIPROT_AUTOSEARCH;
 251   }
 252
 253   @Override
 254   protected void showHelp()
 255   {
 256     try
 257     {
 258       Help.showHelpWindow(HelpId.UniprotFts);
 259     } catch (HelpSetException e1)
 260     {
 261       e1.printStackTrace();
 262     }
 263   }
 264 }