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     errorWarning.setLength(0);
  65     lbl_warning.setVisible(false);
  66     btn_ok.setEnabled(false);
  67     boolean allowEmptySequence = false;
  68     mainFrame.setTitle(MessageManager
  69             .getString("label.pdb_sequence_getcher"));
  70     tbl_summary.setModel(new DefaultTableModel());
  71     if (txt_search.getText().trim().length() > 0)
  72     {
  73       long startTime = System.currentTimeMillis();
  74
  75       String searchTarget = ((PDBDocField) cmb_searchTarget
  76               .getSelectedItem()).getCode();
  77
  78       wantedFields = PDBDocFieldPreferences
  79               .getSearchSummaryFields();
  80
  81       String searchTerm = decodeSearchTerm(txt_search.getText(),
  82               searchTarget);
  83
  84       PDBRestRequest request = new PDBRestRequest();
  85       request.setAllowEmptySeq(allowEmptySequence);
  86       request.setResponseSize(100);
  87       request.setFieldToSearchBy("(" + searchTarget + ":");
  88       request.setSearchTerm(searchTerm + ")");
  89       request.setWantedFields(wantedFields);
  90       // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
  91       PDBRestClient pdbRestCleint = new PDBRestClient();
  92       PDBRestResponse resultList;
  93       try
  94       {
  95         resultList = pdbRestCleint.executeRequest(request);
  96       } catch (Exception e)
  97       {
  98         // System.out.println(">>>>>>>>>>>>>>>" + e.getMessage());
  99         // JOptionPane.showMessageDialog(this, e.getMessage(),
 100         // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
 101         e.printStackTrace();
 102         errorWarning.append(e.getMessage());
 103         checkForErrors();
 104         return;
 105       }
 106
 107       if (resultList.getSearchSummary() != null)
 108       {
 109         tbl_summary.setModel(PDBRestResponse.getTableModel(request,
 110                 resultList.getSearchSummary()));
 111       }
 112
 113       long endTime = System.currentTimeMillis();
 114       int resultSetCount = resultList.getNumberOfItemsFound();
 115       String result = (resultSetCount > 1) ? MessageManager
 116               .getString("label.results") : MessageManager
 117               .getString("label.result");
 118       mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
 119               + " (" + (endTime - startTime) + " milli secs)");
 120     }
 121   }
 122
 123   public static String decodeSearchTerm(String enteredText,
 124           String targetField)
 125   {
 126     String foundSearchTerms = enteredText;
 127     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 128     if (enteredText.contains(";"))
 129     {
 130       String[] searchTerms = enteredText.split(";");
 131       for (String searchTerm : searchTerms)
 132       {
 133         if (searchTerm.contains(":"))
 134         {
 135           foundSearchTermsBuilder.append(targetField).append(":")
 136                   .append(searchTerm.split(":")[0]).append(" OR ");
 137         }
 138         else
 139         {
 140           foundSearchTermsBuilder.append(targetField).append(":")
 141                   .append(searchTerm).append(" OR ");
 142         }
 143       }
 144       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 145       foundSearchTerms = foundSearchTermsBuilder.toString();
 146       if (foundSearchTerms.contains(" OR "))
 147       {
 148         foundSearchTerms = foundSearchTerms.substring(
 149                 targetField.length() + 1, endIndex);
 150       }
 151     }
 152     else if (enteredText.contains(":"))
 153     {
 154       foundSearchTerms = foundSearchTerms.split(":")[0];
 155     }
 156     return foundSearchTerms;
 157   }
 158
 159
 160   @Override
 161   public void btn_ok_ActionPerformed()
 162   {
 163     loadSelectedPDBSequencesToAlignment();
 164   }
 165
 166   @Override
 167   public void btn_back_ActionPerformed()
 168   {
 169     mainFrame.dispose();
 170     new SequenceFetcher(progressIdicator);
 171   }
 172
 173   @Override
 174   public void btn_cancel_ActionPerformed()
 175   {
 176     mainFrame.dispose();
 177   }
 178
 179   public void transferToSequenceFetcher(String ids)
 180   {
 181     // mainFrame.dispose();
 182     seqFetcher.textArea.setText(ids);
 183     Thread worker = new Thread(seqFetcher);
 184     worker.start();
 185   }
 186
 187   /**
 188    * Add the discovered/selected sequences to a target alignment window
 189    */
 190   public void loadSelectedPDBSequencesToAlignment()
 191   {
 192     // mainFrame.dispose();
 193     StringBuilder selectedIds = new StringBuilder();
 194     HashSet<String> selectedIdsSet = new HashSet<String>();
 195     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 196     int[] selectedRows = tbl_summary.getSelectedRows();
 197     for (int summaryRow : selectedRows)
 198     {
 199       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 200               .toString();
 201       String searchTerm = txt_search.getText();
 202       selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
 203     }
 204
 205     for (String selectedId : selectedIdsSet)
 206     {
 207       selectedIds.append(selectedId).append(";");
 208     }
 209
 210     String ids = selectedIds.toString();
 211     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 212     seqFetcher.textArea.setText(ids);
 213     Thread worker = new Thread(seqFetcher);
 214     worker.start();
 215   }
 216
 217   public static String getPDBIdwithSpecifiedChain(String pdbId,
 218           String searchTerm)
 219   {
 220     String pdbIdWithChainCode = "";
 221     if (searchTerm.contains(";"))
 222     {
 223       String[] foundTerms = searchTerm.split(";");
 224       for (String foundTerm : foundTerms)
 225       {
 226         if (foundTerm.contains(pdbId))
 227         {
 228           pdbIdWithChainCode = foundTerm;
 229         }
 230       }
 231     }
 232     else if (searchTerm.contains(pdbId))
 233     {
 234       pdbIdWithChainCode = searchTerm;
 235     }
 236     else
 237     {
 238       pdbIdWithChainCode = pdbId;
 239     }
 240     return pdbIdWithChainCode;
 241   }
 242
 243   /**
 244    * Populates search target combo-box options
 245    */
 246   public void populateCmbSearchTargetOptions()
 247   {
 248     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 249     searchableTargets.add(PDBDocField.PDB_ID);
 250     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 251     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 252     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 253     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 254     searchableTargets.add(PDBDocField.GENE_NAME);
 255     searchableTargets.add(PDBDocField.GENUS);
 256     searchableTargets.add(PDBDocField.ALL);
 257
 258     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 259     {
 260       @Override
 261       public int compare(PDBDocField o1, PDBDocField o2)
 262       {
 263         return o1.getName().compareTo(o2.getName());
 264       }
 265     });
 266
 267     for (PDBDocField searchTarget : searchableTargets)
 268     {
 269       cmb_searchTarget.addItem(searchTarget);
 270     }
 271   }
 272
 273   public void checkForErrors()
 274   {
 275     lbl_warning.setVisible(false);
 276     if (errorWarning.length() > 0)
 277     {
 278       lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
 279               errorWarning.toString()));
 280       lbl_warning.setVisible(true);
 281     }
 282   }
 283 }