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