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