src/jalview/gui/PDBSearchPanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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   /**
  59    * Action performed when an input is detected on txt_search field.
  60    */
  61   @Override
  62   public void txt_search_ActionPerformed()
  63   {
  64     new Thread()
  65     {
  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           long endTime = System.currentTimeMillis();
 116           int resultSetCount = resultList.getNumberOfItemsFound();
 117           String result = (resultSetCount > 1) ? MessageManager
 118                   .getString("label.results") : MessageManager
 119                   .getString("label.result");
 120           mainFrame.setTitle(frameTitle + " - " + resultSetCount + " "
 121                   + result + " (" + (endTime - startTime) + " milli secs)");
 122           lbl_loading.setVisible(false);
 123         }
 124       }
 125     }.start();
 126   }
 127
 128   public static String decodeSearchTerm(String enteredText,
 129           String targetField)
 130   {
 131     String foundSearchTerms = enteredText;
 132     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 133     if (enteredText.contains(";"))
 134     {
 135       String[] searchTerms = enteredText.split(";");
 136       for (String searchTerm : searchTerms)
 137       {
 138         if (searchTerm.contains(":"))
 139         {
 140           foundSearchTermsBuilder.append(targetField).append(":")
 141                   .append(searchTerm.split(":")[0]).append(" OR ");
 142         }
 143         else
 144         {
 145           foundSearchTermsBuilder.append(targetField).append(":")
 146                   .append(searchTerm).append(" OR ");
 147         }
 148       }
 149       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 150       foundSearchTerms = foundSearchTermsBuilder.toString();
 151       if (foundSearchTerms.contains(" OR "))
 152       {
 153         foundSearchTerms = foundSearchTerms.substring(
 154                 targetField.length() + 1, endIndex);
 155       }
 156     }
 157     else if (enteredText.contains(":"))
 158     {
 159       foundSearchTerms = foundSearchTerms.split(":")[0];
 160     }
 161     return foundSearchTerms;
 162   }
 163
 164
 165   @Override
 166   public void btn_ok_ActionPerformed()
 167   {
 168     loadSelectedPDBSequencesToAlignment();
 169   }
 170
 171   @Override
 172   public void btn_back_ActionPerformed()
 173   {
 174     mainFrame.dispose();
 175     new SequenceFetcher(progressIdicator);
 176   }
 177
 178   @Override
 179   public void btn_cancel_ActionPerformed()
 180   {
 181     mainFrame.dispose();
 182   }
 183
 184   public void transferToSequenceFetcher(String ids)
 185   {
 186     // mainFrame.dispose();
 187     seqFetcher.textArea.setText(ids);
 188     Thread worker = new Thread(seqFetcher);
 189     worker.start();
 190   }
 191
 192   /**
 193    * Add the discovered/selected sequences to a target alignment window
 194    */
 195   public void loadSelectedPDBSequencesToAlignment()
 196   {
 197     // mainFrame.dispose();
 198     disableActionButtons();
 199     StringBuilder selectedIds = new StringBuilder();
 200     HashSet<String> selectedIdsSet = new HashSet<String>();
 201     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 202     int[] selectedRows = tbl_summary.getSelectedRows();
 203     for (int summaryRow : selectedRows)
 204     {
 205       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 206               .toString();
 207       String searchTerm = txt_search.getText();
 208       selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
 209     }
 210
 211     for (String selectedId : selectedIdsSet)
 212     {
 213       selectedIds.append(selectedId).append(";");
 214     }
 215
 216     String ids = selectedIds.toString();
 217     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 218     seqFetcher.textArea.setText(ids);
 219     Thread worker = new Thread(seqFetcher);
 220     worker.start();
 221     delayAndEnableActionButtons();
 222
 223   }
 224
 225   private void disableActionButtons()
 226   {
 227     btn_ok.setEnabled(false);
 228     btn_back.setEnabled(false);
 229     btn_cancel.setEnabled(false);
 230   }
 231
 232   private void delayAndEnableActionButtons()
 233   {
 234     new Thread()
 235     {
 236       public void run()
 237       {
 238         try
 239         {
 240           Thread.sleep(1500);
 241         } catch (InterruptedException e)
 242         {
 243           e.printStackTrace();
 244         }
 245         btn_ok.setEnabled(true);
 246         btn_back.setEnabled(true);
 247         btn_cancel.setEnabled(true);
 248       }
 249     }.start();
 250   }
 251
 252   public static String getPDBIdwithSpecifiedChain(String pdbId,
 253           String searchTerm)
 254   {
 255     String pdbIdWithChainCode = "";
 256     if (searchTerm.contains(";"))
 257     {
 258       String[] foundTerms = searchTerm.split(";");
 259       for (String foundTerm : foundTerms)
 260       {
 261         if (foundTerm.contains(pdbId))
 262         {
 263           pdbIdWithChainCode = foundTerm;
 264         }
 265       }
 266     }
 267     else if (searchTerm.contains(pdbId))
 268     {
 269       pdbIdWithChainCode = searchTerm;
 270     }
 271     else
 272     {
 273       pdbIdWithChainCode = pdbId;
 274     }
 275     return pdbIdWithChainCode;
 276   }
 277
 278   /**
 279    * Populates search target combo-box options
 280    */
 281   public void populateCmbSearchTargetOptions()
 282   {
 283     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 284     searchableTargets.add(PDBDocField.PDB_ID);
 285     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 286     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 287     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 288     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 289     searchableTargets.add(PDBDocField.GENE_NAME);
 290     searchableTargets.add(PDBDocField.GENUS);
 291     searchableTargets.add(PDBDocField.ALL);
 292
 293     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 294     {
 295       @Override
 296       public int compare(PDBDocField o1, PDBDocField o2)
 297       {
 298         return o1.getName().compareTo(o2.getName());
 299       }
 300     });
 301
 302     for (PDBDocField searchTarget : searchableTargets)
 303     {
 304       cmb_searchTarget.addItem(searchTarget);
 305     }
 306   }
 307
 308   public void checkForErrors()
 309   {
 310     lbl_warning.setVisible(false);
 311     if (errorWarning.length() > 0)
 312     {
 313       lbl_loading.setVisible(false);
 314       lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
 315               errorWarning.toString()));
 316       lbl_warning.setVisible(true);
 317     }
 318   }
 319 }