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