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.JOptionPane;
  40 import javax.swing.table.DefaultTableModel;
  41
  42 @SuppressWarnings("serial")
  43 public class PDBSearchPanel extends GPDBSearchPanel
  44 {
  45   private SequenceFetcher seqFetcher;
  46
  47   private IProgressIndicator progressIdicator;
  48
  49   private Collection<PDBDocField> wantedFields;
  50
  51   public PDBSearchPanel(SequenceFetcher seqFetcher)
  52   {
  53     this.seqFetcher = seqFetcher;
  54     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  55             .getProgressIndicator();
  56   }
  57
  58
  59   /**
  60    * Action performed when an input is detected on txt_search field.
  61    */
  62   @Override
  63   public void txt_search_ActionPerformed()
  64   {
  65     btn_ok.setEnabled(false);
  66     boolean allowEmptySequence = false;
  67     mainFrame.setTitle(MessageManager
  68             .getString("label.pdb_sequence_getcher"));
  69     tbl_summary.setModel(new DefaultTableModel());
  70     if (txt_search.getText().trim().length() > 0)
  71     {
  72       long startTime = System.currentTimeMillis();
  73
  74       String searchTarget = ((PDBDocField) cmb_searchTarget
  75               .getSelectedItem()).getCode();
  76
  77       wantedFields = PDBDocFieldPreferences
  78               .getSearchSummaryFields();
  79
  80       String searchTerm = decodeSearchTerm(txt_search.getText(),
  81               searchTarget);
  82
  83       PDBRestRequest request = new PDBRestRequest();
  84       request.setAllowEmptySeq(allowEmptySequence);
  85       request.setResponseSize(100);
  86       request.setFieldToSearchBy("(" + searchTarget + ":");
  87       request.setSearchTerm(searchTerm + ")");
  88       request.setWantedFields(wantedFields);
  89       // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
  90       PDBRestClient pdbRestCleint = new PDBRestClient();
  91       PDBRestResponse resultList;
  92       try
  93       {
  94         resultList = pdbRestCleint.executeRequest(request);
  95       } catch (Exception e)
  96       {
  97         // System.out.println(">>>>>>>>>>>>>>>" + e.getMessage());
  98         JOptionPane.showMessageDialog(this, e.getMessage(),
  99                 "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
 100         return;
 101       }
 102
 103       if (resultList.getSearchSummary() != null)
 104       {
 105         tbl_summary.setModel(PDBRestResponse.getTableModel(request,
 106                 resultList.getSearchSummary()));
 107       }
 108
 109       long endTime = System.currentTimeMillis();
 110       int resultSetCount = resultList.getNumberOfItemsFound();
 111       String result = (resultSetCount > 1) ? MessageManager
 112               .getString("label.results") : MessageManager
 113               .getString("label.result");
 114       mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
 115               + " (" + (endTime - startTime) + " milli secs)");
 116     }
 117   }
 118
 119   public static String decodeSearchTerm(String enteredText,
 120           String targetField)
 121   {
 122     String foundSearchTerms = enteredText;
 123     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 124     if (enteredText.contains(";"))
 125     {
 126       String[] searchTerms = enteredText.split(";");
 127       for (String searchTerm : searchTerms)
 128       {
 129         if (searchTerm.contains(":"))
 130         {
 131           foundSearchTermsBuilder.append(targetField).append(":")
 132                   .append(searchTerm.split(":")[0]).append(" OR ");
 133         }
 134         else
 135         {
 136           foundSearchTermsBuilder.append(targetField).append(":")
 137                   .append(searchTerm).append(" OR ");
 138         }
 139       }
 140       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 141       foundSearchTerms = foundSearchTermsBuilder.toString();
 142       if (foundSearchTerms.contains(" OR "))
 143       {
 144         foundSearchTerms = foundSearchTerms.substring(
 145                 targetField.length() + 1, endIndex);
 146       }
 147     }
 148     else if (enteredText.contains(":"))
 149     {
 150       foundSearchTerms = foundSearchTerms.split(":")[0];
 151     }
 152     return foundSearchTerms;
 153   }
 154
 155
 156   @Override
 157   public void btn_ok_ActionPerformed()
 158   {
 159     loadSelectedPDBSequencesToAlignment();
 160   }
 161
 162   @Override
 163   public void btn_back_ActionPerformed()
 164   {
 165     mainFrame.dispose();
 166     new SequenceFetcher(progressIdicator);
 167   }
 168
 169   @Override
 170   public void btn_cancel_ActionPerformed()
 171   {
 172     mainFrame.dispose();
 173   }
 174
 175   /**
 176    * Add the discovered/selected sequences to a target alignment window
 177    */
 178   public void loadSelectedPDBSequencesToAlignment()
 179   {
 180     mainFrame.dispose();
 181     StringBuilder selectedIds = new StringBuilder();
 182     HashSet<String> selectedIdsSet = new HashSet<String>();
 183     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 184     int[] selectedRows = tbl_summary.getSelectedRows();
 185     for (int summaryRow : selectedRows)
 186     {
 187       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 188               .toString();
 189       String searchTerm = txt_search.getText();
 190       selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
 191     }
 192
 193     for (String selectedId : selectedIdsSet)
 194     {
 195       selectedIds.append(selectedId).append(";");
 196     }
 197
 198     String ids = selectedIds.toString();
 199     System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 200     seqFetcher.textArea.setText(ids);
 201     Thread worker = new Thread(seqFetcher);
 202     worker.start();
 203   }
 204
 205   public static String getPDBIdwithSpecifiedChain(String pdbId,
 206           String searchTerm)
 207   {
 208     String pdbIdWithChainCode = "";
 209     if (searchTerm.contains(";"))
 210     {
 211       String[] foundTerms = searchTerm.split(";");
 212       for (String foundTerm : foundTerms)
 213       {
 214         if (foundTerm.contains(pdbId))
 215         {
 216           pdbIdWithChainCode = foundTerm;
 217         }
 218       }
 219     }
 220     else if (searchTerm.contains(pdbId))
 221     {
 222       pdbIdWithChainCode = searchTerm;
 223     }
 224     else
 225     {
 226       pdbIdWithChainCode = pdbId;
 227     }
 228     return pdbIdWithChainCode;
 229   }
 230
 231   /**
 232    * Populates search target combo-box options
 233    */
 234   public void populateCmbSearchTargetOptions()
 235   {
 236     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 237     searchableTargets.add(PDBDocField.PDB_ID);
 238     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 239     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 240     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 241     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 242     searchableTargets.add(PDBDocField.GENE_NAME);
 243     searchableTargets.add(PDBDocField.GENUS);
 244     searchableTargets.add(PDBDocField.ALL);
 245
 246     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 247     {
 248       @Override
 249       public int compare(PDBDocField o1, PDBDocField o2)
 250       {
 251         return o1.getName().compareTo(o2.getName());
 252       }
 253     });
 254
 255     for (PDBDocField searchTarget : searchableTargets)
 256     {
 257       cmb_searchTarget.addItem(searchTarget);
 258     }
 259   }
 260
 261 }