src/jalview/gui/PDBSearchPanel.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.gui;
  23
  24 import jalview.jbgui.GPDBSearchPanel;
  25 import jalview.jbgui.PDBDocFieldPreferences;
  26 import jalview.util.MessageManager;
  27 import jalview.ws.dbsources.PDBRestClient;
  28 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
  29 import jalview.ws.uimodel.PDBRestRequest;
  30 import jalview.ws.uimodel.PDBRestResponse;
  31
  32 import java.util.ArrayList;
  33 import java.util.Collection;
  34 import java.util.Collections;
  35 import java.util.Comparator;
  36 import java.util.HashSet;
  37 import java.util.List;
  38
  39 import javax.swing.table.DefaultTableModel;
  40
  41 @SuppressWarnings("serial")
  42 public class PDBSearchPanel extends GPDBSearchPanel
  43 {
  44   private SequenceFetcher seqFetcher;
  45
  46   private IProgressIndicator progressIdicator;
  47
  48   private Collection<PDBDocField> wantedFields;
  49
  50   public PDBSearchPanel(SequenceFetcher seqFetcher)
  51   {
  52     this.seqFetcher = seqFetcher;
  53     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  54             .getProgressIndicator();
  55   }
  56
  57   /**
  58    * Action performed when an input is detected on txt_search field.
  59    */
  60   @Override
  61   public void txt_search_ActionPerformed()
  62   {
  63     new Thread()
  64     {
  65       @Override
  66       public void run()
  67       {
  68         lbl_loading.setVisible(false);
  69         errorWarning.setLength(0);
  70         lbl_warning.setVisible(false);
  71         btn_ok.setEnabled(false);
  72         boolean allowEmptySequence = false;
  73         mainFrame.setTitle(MessageManager
  74                 .getString("label.pdb_sequence_getcher"));
  75         tbl_summary.setModel(new DefaultTableModel());
  76         if (txt_search.getText().trim().length() > 0)
  77         {
  78           lbl_loading.setVisible(true);
  79           long startTime = System.currentTimeMillis();
  80
  81           String searchTarget = ((PDBDocField) cmb_searchTarget
  82                   .getSelectedItem()).getCode();
  83
  84           wantedFields = PDBDocFieldPreferences.getSearchSummaryFields();
  85
  86           String searchTerm = decodeSearchTerm(txt_search.getText(),
  87                   searchTarget);
  88
  89           PDBRestRequest request = new PDBRestRequest();
  90           request.setAllowEmptySeq(allowEmptySequence);
  91           request.setResponseSize(100);
  92           request.setFieldToSearchBy("(" + searchTarget + ":");
  93           request.setSearchTerm(searchTerm + ")");
  94           request.setWantedFields(wantedFields);
  95           // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
  96           PDBRestClient pdbRestCleint = new PDBRestClient();
  97           PDBRestResponse resultList;
  98           try
  99           {
 100             resultList = pdbRestCleint.executeRequest(request);
 101           } catch (Exception e)
 102           {
 103             // e.printStackTrace();
 104             errorWarning.append(e.getMessage());
 105             checkForErrors();
 106             return;
 107           }
 108
 109           if (resultList.getSearchSummary() != null)
 110           {
 111             tbl_summary.setModel(PDBRestResponse.getTableModel(request,
 112                     resultList.getSearchSummary()));
 113           }
 114
 115           PDBRestResponse.configureTableColumn(tbl_summary, wantedFields);
 116
 117           long endTime = System.currentTimeMillis();
 118           int resultSetCount = resultList.getNumberOfItemsFound();
 119           String result = (resultSetCount > 1) ? MessageManager
 120                   .getString("label.results") : MessageManager
 121                   .getString("label.result");
 122           mainFrame.setTitle(frameTitle + " - " + resultSetCount + " "
 123                   + result + " (" + (endTime - startTime) + " milli secs)");
 124           lbl_loading.setVisible(false);
 125         }
 126       }
 127     }.start();
 128   }
 129
 130   public static String decodeSearchTerm(String enteredText,
 131           String targetField)
 132   {
 133     String foundSearchTerms = enteredText;
 134     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 135     if (enteredText.contains(";"))
 136     {
 137       String[] searchTerms = enteredText.split(";");
 138       for (String searchTerm : searchTerms)
 139       {
 140         if (searchTerm.contains(":"))
 141         {
 142           foundSearchTermsBuilder.append(targetField).append(":")
 143                   .append(searchTerm.split(":")[0]).append(" OR ");
 144         }
 145         else
 146         {
 147           foundSearchTermsBuilder.append(targetField).append(":")
 148                   .append(searchTerm).append(" OR ");
 149         }
 150       }
 151       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 152       foundSearchTerms = foundSearchTermsBuilder.toString();
 153       if (foundSearchTerms.contains(" OR "))
 154       {
 155         foundSearchTerms = foundSearchTerms.substring(
 156                 targetField.length() + 1, endIndex);
 157       }
 158     }
 159     else if (enteredText.contains(":"))
 160     {
 161       foundSearchTerms = foundSearchTerms.split(":")[0];
 162     }
 163     return foundSearchTerms;
 164   }
 165
 166   @Override
 167   public void btn_ok_ActionPerformed()
 168   {
 169     loadSelectedPDBSequencesToAlignment();
 170   }
 171
 172   @Override
 173   public void btn_back_ActionPerformed()
 174   {
 175     mainFrame.dispose();
 176     new SequenceFetcher(progressIdicator);
 177   }
 178
 179   @Override
 180   public void btn_cancel_ActionPerformed()
 181   {
 182     mainFrame.dispose();
 183   }
 184
 185   @Override
 186   public void transferToSequenceFetcher(String ids)
 187   {
 188     // mainFrame.dispose();
 189     seqFetcher.textArea.setText(ids);
 190     Thread worker = new Thread(seqFetcher);
 191     worker.start();
 192   }
 193
 194   /**
 195    * Add the discovered/selected sequences to a target alignment window
 196    */
 197   public void loadSelectedPDBSequencesToAlignment()
 198   {
 199     // mainFrame.dispose();
 200     disableActionButtons();
 201     StringBuilder selectedIds = new StringBuilder();
 202     HashSet<String> selectedIdsSet = new HashSet<String>();
 203     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 204     int[] selectedRows = tbl_summary.getSelectedRows();
 205     for (int summaryRow : selectedRows)
 206     {
 207       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 208               .toString();
 209       String searchTerm = txt_search.getText();
 210       selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
 211     }
 212
 213     for (String selectedId : selectedIdsSet)
 214     {
 215       selectedIds.append(selectedId).append(";");
 216     }
 217
 218     String ids = selectedIds.toString();
 219     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 220     seqFetcher.textArea.setText(ids);
 221     Thread worker = new Thread(seqFetcher);
 222     worker.start();
 223     delayAndEnableActionButtons();
 224
 225   }
 226
 227   private void disableActionButtons()
 228   {
 229     btn_ok.setEnabled(false);
 230     btn_back.setEnabled(false);
 231     btn_cancel.setEnabled(false);
 232   }
 233
 234   private void delayAndEnableActionButtons()
 235   {
 236     new Thread()
 237     {
 238       @Override
 239       public void run()
 240       {
 241         try
 242         {
 243           Thread.sleep(1500);
 244         } catch (InterruptedException e)
 245         {
 246           e.printStackTrace();
 247         }
 248         btn_ok.setEnabled(true);
 249         btn_back.setEnabled(true);
 250         btn_cancel.setEnabled(true);
 251       }
 252     }.start();
 253   }
 254
 255   public static String getPDBIdwithSpecifiedChain(String pdbId,
 256           String searchTerm)
 257   {
 258     String pdbIdWithChainCode = "";
 259     if (searchTerm.contains(";"))
 260     {
 261       String[] foundTerms = searchTerm.split(";");
 262       for (String foundTerm : foundTerms)
 263       {
 264         if (foundTerm.contains(pdbId))
 265         {
 266           pdbIdWithChainCode = foundTerm;
 267         }
 268       }
 269     }
 270     else if (searchTerm.contains(pdbId))
 271     {
 272       pdbIdWithChainCode = searchTerm;
 273     }
 274     else
 275     {
 276       pdbIdWithChainCode = pdbId;
 277     }
 278     return pdbIdWithChainCode;
 279   }
 280
 281   /**
 282    * Populates search target combo-box options
 283    */
 284   @Override
 285   public void populateCmbSearchTargetOptions()
 286   {
 287     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 288     searchableTargets.add(PDBDocField.PDB_ID);
 289     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 290     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 291     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 292     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 293     searchableTargets.add(PDBDocField.GENE_NAME);
 294     searchableTargets.add(PDBDocField.GENUS);
 295     searchableTargets.add(PDBDocField.ALL);
 296
 297     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 298     {
 299       @Override
 300       public int compare(PDBDocField o1, PDBDocField o2)
 301       {
 302         return o1.getName().compareTo(o2.getName());
 303       }
 304     });
 305
 306     for (PDBDocField searchTarget : searchableTargets)
 307     {
 308       cmb_searchTarget.addItem(searchTarget);
 309     }
 310   }
 311
 312   public void checkForErrors()
 313   {
 314     lbl_warning.setVisible(false);
 315     if (errorWarning.length() > 0)
 316     {
 317       lbl_loading.setVisible(false);
 318       lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
 319               errorWarning.toString()));
 320       lbl_warning.setVisible(true);
 321     }
 322   }
 323 }