src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java

   1 package jalview.fts.service.threedbeacons;
   2
   3 import java.util.HashMap;
   4 import java.util.HashSet;
   5 import java.util.Map;
   6
   7 import jalview.fts.api.FTSDataColumnI;
   8 import jalview.fts.api.FTSRestClientI;
   9 import jalview.fts.core.FTSRestRequest;
  10 import jalview.fts.core.FTSRestResponse;
  11 import jalview.fts.core.GFTSPanel;
  12 import jalview.fts.service.pdb.PDBFTSRestClient;
  13 import jalview.gui.SequenceFetcher;
  14 import jalview.util.MessageManager;
  15
  16 @SuppressWarnings("serial")
  17 public class TDBeaconsFTSPanel extends GFTSPanel
  18 {
  19   private static String defaultFTSFrameTitle = MessageManager
  20           .getString("label.threedb_sequence_fetcher");
  21
  22   private static Map<String, Integer> tempUserPrefs = new HashMap<>();
  23
  24   private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";
  25
  26   private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
  27
  28   public TDBeaconsFTSPanel(SequenceFetcher fetcher)
  29   {
  30     super(fetcher);
  31     pageLimit = TDBeaconsFTSRestClient.getInstance().getDefaultResponsePageSize();
  32     this.seqFetcher = fetcher;
  33     this.progressIndicator = (fetcher == null) ? null
  34             : fetcher.getProgressIndicator();
  35   }
  36
  37   @Override
  38   public void searchAction(boolean isFreshSearch)
  39   {
  40     mainFrame.requestFocusInWindow();
  41     if (isFreshSearch)
  42     {
  43       offSet = 0;
  44     }
  45     new Thread()
  46     {
  47       @Override
  48       public void run()
  49       {
  50         reset();
  51         boolean allowEmptySequence = false;
  52         if (getTypedText().length() > 0)
  53         {
  54           setSearchInProgress(true);
  55           long startTime = System.currentTimeMillis();
  56
  57           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  58                   .getSelectedItem()).getCode();
  59           wantedFields = TDBeaconsFTSRestClient.getInstance()
  60                   .getAllDefaultDisplayedFTSDataColumns();
  61           String searchTerm = getTypedText(); // to add : decodeSearchTerm
  62
  63           FTSRestRequest request = new FTSRestRequest();
  64           request.setAllowEmptySeq(allowEmptySequence);
  65           request.setResponseSize(100);
  66           request.setFieldToSearchBy("(" + searchTarget + ":");
  67           request.setSearchTerm(searchTerm + ")");
  68           request.setOffSet(offSet);
  69           request.setWantedFields(wantedFields);
  70           FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient.getInstance();
  71           FTSRestResponse resultList;
  72           try
  73           {
  74             resultList = tdbRestClient.executeRequest(request);
  75           } catch (Exception e)
  76           {
  77             setErrorMessage(e.getMessage());
  78             checkForErrors();
  79             setSearchInProgress(false);
  80             return;
  81           }
  82
  83           if (resultList.getSearchSummary() != null
  84                   && resultList.getSearchSummary().size() > 0)
  85           {
  86             getResultTable().setModel(FTSRestResponse.getTableModel(request,
  87                     resultList.getSearchSummary()));
  88             FTSRestResponse.configureTableColumn(getResultTable(),
  89                     wantedFields, tempUserPrefs);
  90             getResultTable().setVisible(true);
  91           }
  92
  93           long endTime = System.currentTimeMillis();
  94           totalResultSetCount = resultList.getNumberOfItemsFound();
  95           resultSetCount = resultList.getSearchSummary() == null ? 0
  96                   : resultList.getSearchSummary().size();
  97           String result = (resultSetCount > 0)
  98                   ? MessageManager.getString("label.results")
  99                   : MessageManager.getString("label.result");
 100
 101           if (isPaginationEnabled() && resultSetCount > 0)
 102           {
 103             String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
 104             String f2 = totalNumberformatter
 105                     .format(Integer.valueOf(offSet + resultSetCount));
 106             String f3 = totalNumberformatter
 107                     .format(Integer.valueOf(totalResultSetCount));
 108             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
 109                     + " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
 110                     + (endTime - startTime) + " milli secs)");
 111           }
 112           else
 113           {
 114             updateSearchFrameTitle(defaultFTSFrameTitle + " - "
 115                     + resultSetCount + " " + result + " ("
 116                     + (endTime - startTime) + " milli secs)");
 117           }
 118
 119           setSearchInProgress(false);
 120           refreshPaginatorState();
 121           updateSummaryTableSelections();
 122         }
 123         txt_search.updateCache();
 124       }
 125     }.start();
 126   }
 127
 128   @Override
 129   public void okAction()
 130   {
 131     // mainFrame.dispose();
 132     disableActionButtons();
 133     StringBuilder selectedIds = new StringBuilder();
 134     HashSet<String> selectedIdsSet = new HashSet<>();
 135     int primaryKeyColIndex = 0;
 136     try
 137     {
 138       primaryKeyColIndex = getFTSRestClient()
 139               .getPrimaryKeyColumIndex(wantedFields, false);
 140     } catch (Exception e)
 141     {
 142       e.printStackTrace();
 143     }
 144     int[] selectedRows = getResultTable().getSelectedRows();
 145     String searchTerm = getTypedText();
 146     for (int summaryRow : selectedRows)
 147     {
 148       String idStr = getResultTable()
 149               .getValueAt(summaryRow, primaryKeyColIndex).toString();
 150       selectedIdsSet.add(searchTerm);
 151     }
 152
 153     for (String idStr : paginatorCart)
 154     {
 155       selectedIdsSet.add(searchTerm);
 156     }
 157
 158     for (String selectedId : selectedIdsSet)
 159     {
 160       selectedIds.append(selectedId).append(";");
 161     }
 162
 163     String ids = selectedIds.toString();
 164     seqFetcher.setQuery(ids);
 165     Thread worker = new Thread(seqFetcher);
 166     worker.start();
 167     delayAndEnableActionButtons();
 168   }
 169
 170   @Override
 171   public FTSRestClientI getFTSRestClient()
 172   {
 173     return TDBeaconsFTSRestClient.getInstance();
 174   }
 175
 176   @Override
 177   public String getFTSFrameTitle()
 178   {
 179     return defaultFTSFrameTitle;
 180   }
 181
 182   @Override
 183   public boolean isPaginationEnabled()
 184   {
 185     return true;
 186   }
 187
 188   @Override
 189   public Map<String, Integer> getTempUserPrefs()
 190   {
 191     return tempUserPrefs;
 192   }
 193
 194   @Override
 195   public String getCacheKey()
 196   {
 197     return THREEDB_FTS_CACHE_KEY;
 198   }
 199
 200   @Override
 201   public String getAutosearchPreference()
 202   {
 203     return THREEDB_AUTOSEARCH;
 204   }
 205
 206   @Override
 207   protected void showHelp()
 208   {
 209     System.out.println("No help implemented yet.");
 210
 211   }
 212
 213 }