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     StringBuilder selectedIds = new StringBuilder();
 199     HashSet<String> selectedIdsSet = new HashSet<String>();
 200     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 201     int[] selectedRows = tbl_summary.getSelectedRows();
 202     for (int summaryRow : selectedRows)
 203     {
 204       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 205               .toString();
 206       String searchTerm = txt_search.getText();
 207       selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
 208     }
 209
 210     for (String selectedId : selectedIdsSet)
 211     {
 212       selectedIds.append(selectedId).append(";");
 213     }
 214
 215     String ids = selectedIds.toString();
 216     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 217     seqFetcher.textArea.setText(ids);
 218     Thread worker = new Thread(seqFetcher);
 219     worker.start();
 220   }
 221
 222   public static String getPDBIdwithSpecifiedChain(String pdbId,
 223           String searchTerm)
 224   {
 225     String pdbIdWithChainCode = "";
 226     if (searchTerm.contains(";"))
 227     {
 228       String[] foundTerms = searchTerm.split(";");
 229       for (String foundTerm : foundTerms)
 230       {
 231         if (foundTerm.contains(pdbId))
 232         {
 233           pdbIdWithChainCode = foundTerm;
 234         }
 235       }
 236     }
 237     else if (searchTerm.contains(pdbId))
 238     {
 239       pdbIdWithChainCode = searchTerm;
 240     }
 241     else
 242     {
 243       pdbIdWithChainCode = pdbId;
 244     }
 245     return pdbIdWithChainCode;
 246   }
 247
 248   /**
 249    * Populates search target combo-box options
 250    */
 251   public void populateCmbSearchTargetOptions()
 252   {
 253     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 254     searchableTargets.add(PDBDocField.PDB_ID);
 255     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 256     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 257     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 258     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 259     searchableTargets.add(PDBDocField.GENE_NAME);
 260     searchableTargets.add(PDBDocField.GENUS);
 261     searchableTargets.add(PDBDocField.ALL);
 262
 263     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 264     {
 265       @Override
 266       public int compare(PDBDocField o1, PDBDocField o2)
 267       {
 268         return o1.getName().compareTo(o2.getName());
 269       }
 270     });
 271
 272     for (PDBDocField searchTarget : searchableTargets)
 273     {
 274       cmb_searchTarget.addItem(searchTarget);
 275     }
 276   }
 277
 278   public void checkForErrors()
 279   {
 280     lbl_warning.setVisible(false);
 281     if (errorWarning.length() > 0)
 282     {
 283       lbl_loading.setVisible(false);
 284       lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
 285               errorWarning.toString()));
 286       lbl_warning.setVisible(true);
 287     }
 288   }
 289 }