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 import javax.swing.table.DefaultTableModel;
  35
  36 @SuppressWarnings("serial")
  37 public class PDBFTSPanel extends GFTSPanel
  38 {
  39
  40   public PDBFTSPanel(SequenceFetcher seqFetcher)
  41   {
  42     this.seqFetcher = seqFetcher;
  43     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  44             .getProgressIndicator();
  45   }
  46
  47
  48   /**
  49    * Action performed when an input is detected on txt_search field.
  50    */
  51   @Override
  52   public void txt_search_ActionPerformed()
  53   {
  54     new Thread()
  55     {
  56       @Override
  57       public void run()
  58       {
  59         lbl_loading.setVisible(false);
  60         errorWarning.setLength(0);
  61         lbl_warning.setVisible(false);
  62         btn_ok.setEnabled(false);
  63         boolean allowEmptySequence = false;
  64         mainFrame.setTitle(getFTSFrameTitle());
  65         tbl_summary.setModel(new DefaultTableModel());
  66         tbl_summary.setVisible(false);
  67         if (txt_search.getText().trim().length() > 0)
  68         {
  69           lbl_loading.setVisible(true);
  70           long startTime = System.currentTimeMillis();
  71
  72           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
  73                   .getSelectedItem()).getCode();
  74
  75           // wantedFields = FTSDataColumnPreferences.getSearchSummaryFields();
  76           wantedFields = PDBFTSRestClient.getInstance()
  77                   .getAllDefaulDisplayedDataColumns();
  78           String searchTerm = decodeSearchTerm(txt_search.getText(),
  79                   searchTarget);
  80
  81           FTSRestRequest request = new FTSRestRequest();
  82           request.setAllowEmptySeq(allowEmptySequence);
  83           request.setResponseSize(100);
  84           request.setFieldToSearchBy("(" + searchTarget + ":");
  85           request.setSearchTerm(searchTerm + ")");
  86           request.setWantedFields(wantedFields);
  87           // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
  88           FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
  89           FTSRestResponse resultList;
  90           try
  91           {
  92             resultList = pdbRestCleint.executeRequest(request);
  93           } catch (Exception e)
  94           {
  95             // e.printStackTrace();
  96             errorWarning.append(e.getMessage());
  97             checkForErrors();
  98             return;
  99           }
 100
 101           if (resultList.getSearchSummary() != null)
 102           {
 103             tbl_summary.setModel(FTSRestResponse.getTableModel(request,
 104                     resultList.getSearchSummary()));
 105             FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
 106             tbl_summary.setVisible(true);
 107           }
 108
 109
 110           long endTime = System.currentTimeMillis();
 111           int resultSetCount = resultList.getNumberOfItemsFound();
 112           String result = (resultSetCount > 1) ? MessageManager
 113                   .getString("label.results") : MessageManager
 114                   .getString("label.result");
 115           mainFrame.setTitle(getFTSFrameTitle() + " - " + resultSetCount
 116                   + " "
 117                   + result + " (" + (endTime - startTime) + " milli secs)");
 118           lbl_loading.setVisible(false);
 119         }
 120       }
 121     }.start();
 122   }
 123
 124   public static String decodeSearchTerm(String enteredText,
 125           String targetField)
 126   {
 127     String foundSearchTerms = enteredText;
 128     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 129     if (enteredText.contains(";"))
 130     {
 131       String[] searchTerms = enteredText.split(";");
 132       for (String searchTerm : searchTerms)
 133       {
 134         if (searchTerm.contains(":"))
 135         {
 136           foundSearchTermsBuilder.append(targetField).append(":")
 137                   .append(searchTerm.split(":")[0]).append(" OR ");
 138         }
 139         else
 140         {
 141           foundSearchTermsBuilder.append(targetField).append(":")
 142                   .append(searchTerm).append(" OR ");
 143         }
 144       }
 145       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 146       foundSearchTerms = foundSearchTermsBuilder.toString();
 147       if (foundSearchTerms.contains(" OR "))
 148       {
 149         foundSearchTerms = foundSearchTerms.substring(
 150                 targetField.length() + 1, endIndex);
 151       }
 152     }
 153     else if (enteredText.contains(":"))
 154     {
 155       foundSearchTerms = foundSearchTerms.split(":")[0];
 156     }
 157     return foundSearchTerms;
 158   }
 159
 160   @Override
 161   public void btn_ok_ActionPerformed()
 162   {
 163     // mainFrame.dispose();
 164     disableActionButtons();
 165     StringBuilder selectedIds = new StringBuilder();
 166     HashSet<String> selectedIdsSet = new HashSet<String>();
 167     int pdbIdCol = 0;
 168     try
 169     {
 170       pdbIdCol = getFTSRestClient().getPrimaryKeyColumIndex(wantedFields,
 171               false);
 172     } catch (Exception e)
 173     {
 174       // TODO Auto-generated catch block
 175       e.printStackTrace();
 176     }
 177     int[] selectedRows = tbl_summary.getSelectedRows();
 178     for (int summaryRow : selectedRows)
 179     {
 180       String idStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 181               .toString();
 182       String searchTerm = txt_search.getText();
 183       selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
 184     }
 185
 186     for (String selectedId : selectedIdsSet)
 187     {
 188       selectedIds.append(selectedId).append(";");
 189     }
 190
 191     String ids = selectedIds.toString();
 192     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 193     seqFetcher.getTextArea().setText(ids);
 194     Thread worker = new Thread(seqFetcher);
 195     worker.start();
 196     delayAndEnableActionButtons();
 197   }
 198
 199
 200   public static String getPDBIdwithSpecifiedChain(String pdbId,
 201           String searchTerm)
 202   {
 203     String pdbIdWithChainCode = "";
 204     if (searchTerm.contains(";"))
 205     {
 206       String[] foundTerms = searchTerm.split(";");
 207       for (String foundTerm : foundTerms)
 208       {
 209         if (foundTerm.contains(pdbId))
 210         {
 211           pdbIdWithChainCode = foundTerm;
 212         }
 213       }
 214     }
 215     else if (searchTerm.contains(pdbId))
 216     {
 217       pdbIdWithChainCode = searchTerm;
 218     }
 219     else
 220     {
 221       pdbIdWithChainCode = pdbId;
 222     }
 223     return pdbIdWithChainCode;
 224   }
 225
 226
 227
 228   @Override
 229   public FTSRestClientI getFTSRestClient()
 230   {
 231     return PDBFTSRestClient.getInstance();
 232   }
 233
 234   @Override
 235   public String getFTSFrameTitle()
 236   {
 237     return MessageManager.getString("label.pdb_sequence_fetcher");
 238   }
 239
 240 }