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             // request.ge
 114             // TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 115             // tbl_pdbDocFieldConfig.getModel());
 116           }
 117
 118           long endTime = System.currentTimeMillis();
 119           int resultSetCount = resultList.getNumberOfItemsFound();
 120           String result = (resultSetCount > 1) ? MessageManager
 121                   .getString("label.results") : MessageManager
 122                   .getString("label.result");
 123           mainFrame.setTitle(frameTitle + " - " + resultSetCount + " "
 124                   + result + " (" + (endTime - startTime) + " milli secs)");
 125           lbl_loading.setVisible(false);
 126         }
 127       }
 128     }.start();
 129   }
 130
 131   public static String decodeSearchTerm(String enteredText,
 132           String targetField)
 133   {
 134     String foundSearchTerms = enteredText;
 135     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 136     if (enteredText.contains(";"))
 137     {
 138       String[] searchTerms = enteredText.split(";");
 139       for (String searchTerm : searchTerms)
 140       {
 141         if (searchTerm.contains(":"))
 142         {
 143           foundSearchTermsBuilder.append(targetField).append(":")
 144                   .append(searchTerm.split(":")[0]).append(" OR ");
 145         }
 146         else
 147         {
 148           foundSearchTermsBuilder.append(targetField).append(":")
 149                   .append(searchTerm).append(" OR ");
 150         }
 151       }
 152       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 153       foundSearchTerms = foundSearchTermsBuilder.toString();
 154       if (foundSearchTerms.contains(" OR "))
 155       {
 156         foundSearchTerms = foundSearchTerms.substring(
 157                 targetField.length() + 1, endIndex);
 158       }
 159     }
 160     else if (enteredText.contains(":"))
 161     {
 162       foundSearchTerms = foundSearchTerms.split(":")[0];
 163     }
 164     return foundSearchTerms;
 165   }
 166
 167   @Override
 168   public void btn_ok_ActionPerformed()
 169   {
 170     loadSelectedPDBSequencesToAlignment();
 171   }
 172
 173   @Override
 174   public void btn_back_ActionPerformed()
 175   {
 176     mainFrame.dispose();
 177     new SequenceFetcher(progressIdicator);
 178   }
 179
 180   @Override
 181   public void btn_cancel_ActionPerformed()
 182   {
 183     mainFrame.dispose();
 184   }
 185
 186   @Override
 187   public void transferToSequenceFetcher(String ids)
 188   {
 189     // mainFrame.dispose();
 190     seqFetcher.textArea.setText(ids);
 191     Thread worker = new Thread(seqFetcher);
 192     worker.start();
 193   }
 194
 195   /**
 196    * Add the discovered/selected sequences to a target alignment window
 197    */
 198   public void loadSelectedPDBSequencesToAlignment()
 199   {
 200     // mainFrame.dispose();
 201     disableActionButtons();
 202     StringBuilder selectedIds = new StringBuilder();
 203     HashSet<String> selectedIdsSet = new HashSet<String>();
 204     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 205     int[] selectedRows = tbl_summary.getSelectedRows();
 206     for (int summaryRow : selectedRows)
 207     {
 208       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 209               .toString();
 210       String searchTerm = txt_search.getText();
 211       selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
 212     }
 213
 214     for (String selectedId : selectedIdsSet)
 215     {
 216       selectedIds.append(selectedId).append(";");
 217     }
 218
 219     String ids = selectedIds.toString();
 220     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 221     seqFetcher.textArea.setText(ids);
 222     Thread worker = new Thread(seqFetcher);
 223     worker.start();
 224     delayAndEnableActionButtons();
 225
 226   }
 227
 228   private void disableActionButtons()
 229   {
 230     btn_ok.setEnabled(false);
 231     btn_back.setEnabled(false);
 232     btn_cancel.setEnabled(false);
 233   }
 234
 235   private void delayAndEnableActionButtons()
 236   {
 237     new Thread()
 238     {
 239       @Override
 240       public void run()
 241       {
 242         try
 243         {
 244           Thread.sleep(1500);
 245         } catch (InterruptedException e)
 246         {
 247           e.printStackTrace();
 248         }
 249         btn_ok.setEnabled(true);
 250         btn_back.setEnabled(true);
 251         btn_cancel.setEnabled(true);
 252       }
 253     }.start();
 254   }
 255
 256   public static String getPDBIdwithSpecifiedChain(String pdbId,
 257           String searchTerm)
 258   {
 259     String pdbIdWithChainCode = "";
 260     if (searchTerm.contains(";"))
 261     {
 262       String[] foundTerms = searchTerm.split(";");
 263       for (String foundTerm : foundTerms)
 264       {
 265         if (foundTerm.contains(pdbId))
 266         {
 267           pdbIdWithChainCode = foundTerm;
 268         }
 269       }
 270     }
 271     else if (searchTerm.contains(pdbId))
 272     {
 273       pdbIdWithChainCode = searchTerm;
 274     }
 275     else
 276     {
 277       pdbIdWithChainCode = pdbId;
 278     }
 279     return pdbIdWithChainCode;
 280   }
 281
 282   /**
 283    * Populates search target combo-box options
 284    */
 285   @Override
 286   public void populateCmbSearchTargetOptions()
 287   {
 288     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 289     searchableTargets.add(PDBDocField.PDB_ID);
 290     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 291     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 292     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 293     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 294     searchableTargets.add(PDBDocField.GENE_NAME);
 295     searchableTargets.add(PDBDocField.GENUS);
 296     searchableTargets.add(PDBDocField.ALL);
 297
 298     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 299     {
 300       @Override
 301       public int compare(PDBDocField o1, PDBDocField o2)
 302       {
 303         return o1.getName().compareTo(o2.getName());
 304       }
 305     });
 306
 307     for (PDBDocField searchTarget : searchableTargets)
 308     {
 309       cmb_searchTarget.addItem(searchTarget);
 310     }
 311   }
 312
 313   public void checkForErrors()
 314   {
 315     lbl_warning.setVisible(false);
 316     if (errorWarning.length() > 0)
 317     {
 318       lbl_loading.setVisible(false);
 319       lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
 320               errorWarning.toString()));
 321       lbl_warning.setVisible(true);
 322     }
 323   }
 324 }