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.JvSummaryTable;
  30 import jalview.gui.SequenceFetcher;
  31 import jalview.util.MessageManager;
  32
  33 import java.util.HashMap;
  34 import java.util.HashSet;
  35 import java.util.Map;
  36
  37 @SuppressWarnings("serial")
  38 public class UniprotFTSPanel extends GFTSPanel
  39 {
  40
  41   private static String defaultFTSFrameTitle = MessageManager
  42           .getString("label.uniprot_sequence_fetcher");
  43
  44
  45   private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
  46
  47   private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
  48
  49   public UniprotFTSPanel(SequenceFetcher seqFetcher)
  50   {
  51     super();
  52     pageLimit = UniProtFTSRestClient.getInstance()
  53             .getDefaultResponsePageSize();
  54     this.seqFetcher = seqFetcher;
  55     this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
  56             .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 uniProtRestCleint = UniProtFTSRestClient
  91                   .getInstance();
  92           FTSRestResponse resultList;
  93           try
  94           {
  95             resultList = uniProtRestCleint.executeRequest(request);
  96           } catch (Exception e)
  97           {
  98             e.printStackTrace();
  99             setErrorMessage(e.getMessage());
 100             checkForErrors();
 101             return;
 102           }
 103
 104           if (resultList.getSearchSummary() != null
 105                   && resultList.getSearchSummary().size() > 0)
 106           {
 107             getResultTable().setModel(
 108                     JvSummaryTable.getTableModel(request,
 109                             resultList.getSearchSummary()));
 110             JvSummaryTable.configureTableColumn(getResultTable(),
 111                     wantedFields, tempUserPrefs);
 112             getResultTable().setVisible(true);
 113           }
 114
 115           long endTime = System.currentTimeMillis();
 116           totalResultSetCount = resultList.getNumberOfItemsFound();
 117           resultSetCount = resultList.getSearchSummary() == null ? 0
 118                   : resultList.getSearchSummary().size();
 119           String result = (resultSetCount > 0) ? MessageManager
 120                   .getString("label.results") : MessageManager
 121                   .getString("label.result");
 122           if (isPaginationEnabled() && resultSetCount > 0)
 123           {
 124             updateSearchFrameTitle(defaultFTSFrameTitle
 125                     + " - "
 126                     + result
 127                     + " "
 128                     + totalNumberformatter.format((Number) (offSet + 1))
 129                     + " to "
 130                     + totalNumberformatter
 131                             .format((Number) (offSet + resultSetCount))
 132                     + " of "
 133                     + totalNumberformatter
 134                             .format((Number) totalResultSetCount) + " "
 135                     + " (" + (endTime - startTime) + " milli secs)");
 136           }
 137           else
 138           {
 139             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 140                     + resultSetCount + " " + result + " ("
 141                     + (endTime - startTime) + " milli secs)");
 142           }
 143           setSearchInProgress(false);
 144           refreshPaginatorState();
 145           updateSummaryTableSelections();
 146         }
 147         txt_search.updateCache();
 148       }
 149     }.start();
 150
 151   }
 152
 153   public String decodeSearchTerm(String enteredText, String targetField)
 154   {
 155     int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
 156             : targetField.length() + 1;
 157     String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
 158             : targetField + ":";
 159     String foundSearchTerms = enteredText;
 160     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 161     if (enteredText.contains(";"))
 162     {
 163       String[] searchTerms = enteredText.split(";");
 164       for (String searchTerm : searchTerms)
 165       {
 166         foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
 167                 .append(" OR ");
 168       }
 169       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 170       foundSearchTerms = foundSearchTermsBuilder.toString();
 171       if (foundSearchTerms.contains(" OR "))
 172       {
 173         foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
 174                 endIndex);
 175       }
 176     }
 177     return foundSearchTerms;
 178   }
 179
 180   @Override
 181   public boolean isPaginationEnabled()
 182   {
 183     return true;
 184   }
 185
 186   @Override
 187   public void okAction()
 188   {
 189     disableActionButtons();
 190     StringBuilder selectedIds = new StringBuilder();
 191     HashSet<String> selectedIdsSet = new HashSet<String>();
 192     int primaryKeyColIndex = 0;
 193     try
 194     {
 195       primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
 196               wantedFields, false);
 197     } catch (Exception e)
 198     {
 199       e.printStackTrace();
 200     }
 201     int[] selectedRows = getResultTable().getSelectedRows();
 202     for (int summaryRow : selectedRows)
 203     {
 204       String idStr = getResultTable().getValueAt(summaryRow,
 205               primaryKeyColIndex).toString();
 206       selectedIdsSet.add(idStr);
 207     }
 208     selectedIdsSet.addAll(paginatorCart);
 209     for (String selectedId : selectedIdsSet)
 210     {
 211       selectedIds.append(selectedId).append(";");
 212     }
 213
 214     String ids = selectedIds.toString();
 215     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 216     seqFetcher.getTextArea().setText(ids);
 217     Thread worker = new Thread(seqFetcher);
 218     worker.start();
 219     delayAndEnableActionButtons();
 220   }
 221
 222   @Override
 223   public FTSRestClientI getFTSRestClient()
 224   {
 225     return UniProtFTSRestClient.getInstance();
 226   }
 227
 228   @Override
 229   public String getFTSFrameTitle()
 230   {
 231     return defaultFTSFrameTitle;
 232   }
 233
 234   @Override
 235   public Map<String, Integer> getTempUserPrefs()
 236   {
 237     return tempUserPrefs;
 238   }
 239
 240   @Override
 241   public String getCacheKey()
 242   {
 243     return UNIPROT_FTS_CACHE_KEY;
 244   }
 245 }