src/jalview/gui/PDBSearchPanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
   3  * Copyright (C) 2015 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       public void run()
  66       {
  67         lbl_loading.setVisible(false);
  68         errorWarning.setLength(0);
  69         lbl_warning.setVisible(false);
  70         btn_ok.setEnabled(false);
  71         boolean allowEmptySequence = false;
  72         mainFrame.setTitle(MessageManager
  73                 .getString("label.pdb_sequence_getcher"));
  74         tbl_summary.setModel(new DefaultTableModel());
  75         if (txt_search.getText().trim().length() > 0)
  76         {
  77           lbl_loading.setVisible(true);
  78           long startTime = System.currentTimeMillis();
  79
  80           String searchTarget = ((PDBDocField) cmb_searchTarget
  81                   .getSelectedItem()).getCode();
  82
  83           wantedFields = PDBDocFieldPreferences.getSearchSummaryFields();
  84
  85           String searchTerm = decodeSearchTerm(txt_search.getText(),
  86                   searchTarget);
  87
  88           PDBRestRequest request = new PDBRestRequest();
  89           request.setAllowEmptySeq(allowEmptySequence);
  90           request.setResponseSize(100);
  91           request.setFieldToSearchBy("(" + searchTarget + ":");
  92           request.setSearchTerm(searchTerm + ")");
  93           request.setWantedFields(wantedFields);
  94           // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
  95           PDBRestClient pdbRestCleint = new PDBRestClient();
  96           PDBRestResponse resultList;
  97           try
  98           {
  99             resultList = pdbRestCleint.executeRequest(request);
 100           } catch (Exception e)
 101           {
 102             // e.printStackTrace();
 103             errorWarning.append(e.getMessage());
 104             checkForErrors();
 105             return;
 106           }
 107
 108           if (resultList.getSearchSummary() != null)
 109           {
 110             tbl_summary.setModel(PDBRestResponse.getTableModel(request,
 111                     resultList.getSearchSummary()));
 112           }
 113
 114           long endTime = System.currentTimeMillis();
 115           int resultSetCount = resultList.getNumberOfItemsFound();
 116           String result = (resultSetCount > 1) ? MessageManager
 117                   .getString("label.results") : MessageManager
 118                   .getString("label.result");
 119           mainFrame.setTitle(frameTitle + " - " + resultSetCount + " "
 120                   + result + " (" + (endTime - startTime) + " milli secs)");
 121           lbl_loading.setVisible(false);
 122         }
 123       }
 124     }.start();
 125   }
 126
 127   public static String decodeSearchTerm(String enteredText,
 128           String targetField)
 129   {
 130     String foundSearchTerms = enteredText;
 131     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 132     if (enteredText.contains(";"))
 133     {
 134       String[] searchTerms = enteredText.split(";");
 135       for (String searchTerm : searchTerms)
 136       {
 137         if (searchTerm.contains(":"))
 138         {
 139           foundSearchTermsBuilder.append(targetField).append(":")
 140                   .append(searchTerm.split(":")[0]).append(" OR ");
 141         }
 142         else
 143         {
 144           foundSearchTermsBuilder.append(targetField).append(":")
 145                   .append(searchTerm).append(" OR ");
 146         }
 147       }
 148       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 149       foundSearchTerms = foundSearchTermsBuilder.toString();
 150       if (foundSearchTerms.contains(" OR "))
 151       {
 152         foundSearchTerms = foundSearchTerms.substring(
 153                 targetField.length() + 1, endIndex);
 154       }
 155     }
 156     else if (enteredText.contains(":"))
 157     {
 158       foundSearchTerms = foundSearchTerms.split(":")[0];
 159     }
 160     return foundSearchTerms;
 161   }
 162
 163   @Override
 164   public void btn_ok_ActionPerformed()
 165   {
 166     loadSelectedPDBSequencesToAlignment();
 167   }
 168
 169   @Override
 170   public void btn_back_ActionPerformed()
 171   {
 172     mainFrame.dispose();
 173     new SequenceFetcher(progressIdicator);
 174   }
 175
 176   @Override
 177   public void btn_cancel_ActionPerformed()
 178   {
 179     mainFrame.dispose();
 180   }
 181
 182   public void transferToSequenceFetcher(String ids)
 183   {
 184     // mainFrame.dispose();
 185     seqFetcher.textArea.setText(ids);
 186     Thread worker = new Thread(seqFetcher);
 187     worker.start();
 188   }
 189
 190   /**
 191    * Add the discovered/selected sequences to a target alignment window
 192    */
 193   public void loadSelectedPDBSequencesToAlignment()
 194   {
 195     // mainFrame.dispose();
 196     disableActionButtons();
 197     StringBuilder selectedIds = new StringBuilder();
 198     HashSet<String> selectedIdsSet = new HashSet<String>();
 199     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 200     int[] selectedRows = tbl_summary.getSelectedRows();
 201     for (int summaryRow : selectedRows)
 202     {
 203       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 204               .toString();
 205       String searchTerm = txt_search.getText();
 206       selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
 207     }
 208
 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.textArea.setText(ids);
 217     Thread worker = new Thread(seqFetcher);
 218     worker.start();
 219     delayAndEnableActionButtons();
 220
 221   }
 222
 223   private void disableActionButtons()
 224   {
 225     btn_ok.setEnabled(false);
 226     btn_back.setEnabled(false);
 227     btn_cancel.setEnabled(false);
 228   }
 229
 230   private void delayAndEnableActionButtons()
 231   {
 232     new Thread()
 233     {
 234       public void run()
 235       {
 236         try
 237         {
 238           Thread.sleep(1500);
 239         } catch (InterruptedException e)
 240         {
 241           e.printStackTrace();
 242         }
 243         btn_ok.setEnabled(true);
 244         btn_back.setEnabled(true);
 245         btn_cancel.setEnabled(true);
 246       }
 247     }.start();
 248   }
 249
 250   public static String getPDBIdwithSpecifiedChain(String pdbId,
 251           String searchTerm)
 252   {
 253     String pdbIdWithChainCode = "";
 254     if (searchTerm.contains(";"))
 255     {
 256       String[] foundTerms = searchTerm.split(";");
 257       for (String foundTerm : foundTerms)
 258       {
 259         if (foundTerm.contains(pdbId))
 260         {
 261           pdbIdWithChainCode = foundTerm;
 262         }
 263       }
 264     }
 265     else if (searchTerm.contains(pdbId))
 266     {
 267       pdbIdWithChainCode = searchTerm;
 268     }
 269     else
 270     {
 271       pdbIdWithChainCode = pdbId;
 272     }
 273     return pdbIdWithChainCode;
 274   }
 275
 276   /**
 277    * Populates search target combo-box options
 278    */
 279   public void populateCmbSearchTargetOptions()
 280   {
 281     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 282     searchableTargets.add(PDBDocField.PDB_ID);
 283     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 284     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 285     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 286     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 287     searchableTargets.add(PDBDocField.GENE_NAME);
 288     searchableTargets.add(PDBDocField.GENUS);
 289     searchableTargets.add(PDBDocField.ALL);
 290
 291     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 292     {
 293       @Override
 294       public int compare(PDBDocField o1, PDBDocField o2)
 295       {
 296         return o1.getName().compareTo(o2.getName());
 297       }
 298     });
 299
 300     for (PDBDocField searchTarget : searchableTargets)
 301     {
 302       cmb_searchTarget.addItem(searchTarget);
 303     }
 304   }
 305
 306   public void checkForErrors()
 307   {
 308     lbl_warning.setVisible(false);
 309     if (errorWarning.length() > 0)
 310     {
 311       lbl_loading.setVisible(false);
 312       lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
 313               errorWarning.toString()));
 314       lbl_warning.setVisible(true);
 315     }
 316   }
 317 }