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.List;
  37
  38 import javax.swing.table.DefaultTableModel;
  39
  40 @SuppressWarnings("serial")
  41 public class PDBSearchPanel extends GPDBSearchPanel
  42 {
  43   private SequenceFetcher seqFetcher;
  44
  45   private IProgressIndicator progressIdicator;
  46
  47   private Collection<PDBDocField> wantedFields;
  48
  49   public PDBSearchPanel(SequenceFetcher seqFetcher)
  50   {
  51     this.seqFetcher = seqFetcher;
  52     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  53             .getProgressIndicator();
  54   }
  55
  56
  57   /**
  58    * Action performed when an input is detected on txt_search field.
  59    */
  60   @Override
  61   public void txt_search_ActionPerformed()
  62   {
  63     boolean allowEmptySequence = false;
  64     mainFrame.setTitle(MessageManager
  65             .getString("label.pdb_sequence_getcher"));
  66     tbl_summary.setModel(new DefaultTableModel());
  67     if (txt_search.getText().trim().length() > 0)
  68     {
  69       long startTime = System.currentTimeMillis();
  70
  71       String searchTarget = ((PDBDocField) cmb_searchTarget
  72               .getSelectedItem()).getCode();
  73
  74       wantedFields = PDBDocFieldPreferences
  75               .getSearchSummaryFields();
  76
  77       String searchTerm = decodeSearchTerm(txt_search.getText(),
  78               searchTarget);
  79
  80       PDBRestRequest request = new PDBRestRequest();
  81       request.setAllowEmptySeq(allowEmptySequence);
  82       request.setResponseSize(100);
  83       request.setFieldToSearchBy("(" + searchTarget + ":");
  84       request.setSearchTerm(searchTerm + ")");
  85       request.setWantedFields(wantedFields);
  86       // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
  87       PDBRestClient pdbRestCleint = new PDBRestClient();
  88       PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
  89       if (resultList.getSearchSummary() != null)
  90       {
  91         tbl_summary.setModel(PDBRestResponse.getTableModel(request,
  92                 resultList.getSearchSummary()));
  93       }
  94
  95       long endTime = System.currentTimeMillis();
  96       int resultSetCount = resultList.getNumberOfItemsFound();
  97       String result = (resultSetCount > 1) ? MessageManager
  98               .getString("label.results") : MessageManager
  99               .getString("label.result");
 100       mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
 101               + " (" + (endTime - startTime) + " milli secs)");
 102     }
 103   }
 104
 105   public static String decodeSearchTerm(String enteredText,
 106           String targetField)
 107   {
 108     String foundSearchTerms = enteredText;
 109     StringBuilder foundSearchTermsBuilder = new StringBuilder();
 110     if (enteredText.contains(";"))
 111     {
 112       String[] searchTerms = enteredText.split(";");
 113       for (String searchTerm : searchTerms)
 114       {
 115         if (searchTerm.contains(":"))
 116         {
 117           foundSearchTermsBuilder.append(targetField).append(":")
 118                   .append(searchTerm.split(":")[0]).append(" OR ");
 119         }
 120         else
 121         {
 122           foundSearchTermsBuilder.append(targetField).append(":")
 123                   .append(searchTerm).append(" OR ");
 124         }
 125       }
 126       int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
 127       foundSearchTerms = foundSearchTermsBuilder.toString();
 128       if (foundSearchTerms.contains(" OR "))
 129       {
 130         foundSearchTerms = foundSearchTerms.substring(
 131                 targetField.length() + 1, endIndex);
 132       }
 133     }
 134     else if (enteredText.contains(":"))
 135     {
 136       foundSearchTerms = foundSearchTerms.split(":")[0];
 137     }
 138     return foundSearchTerms;
 139   }
 140
 141
 142   @Override
 143   public void btn_ok_ActionPerformed()
 144   {
 145     loadSelectedPDBSequencesToAlignment();
 146   }
 147
 148   @Override
 149   public void btn_back_ActionPerformed()
 150   {
 151     mainFrame.dispose();
 152     new SequenceFetcher(progressIdicator);
 153   }
 154
 155   @Override
 156   public void btn_cancel_ActionPerformed()
 157   {
 158     mainFrame.dispose();
 159   }
 160
 161   /**
 162    * Add the discovered/selected sequences to a target alignment window
 163    */
 164   public void loadSelectedPDBSequencesToAlignment()
 165   {
 166     mainFrame.dispose();
 167     StringBuilder selectedIds = new StringBuilder();
 168     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 169     int[] selectedRows = tbl_summary.getSelectedRows();
 170     for (int summaryRow : selectedRows)
 171     {
 172       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 173               .toString();
 174
 175       String searchTerm = txt_search.getText();
 176       selectedIds.append(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm))
 177               .append(";");
 178     }
 179
 180     String ids = selectedIds.toString();
 181     // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
 182     seqFetcher.textArea.setText(ids);
 183     Thread worker = new Thread(seqFetcher);
 184     worker.start();
 185   }
 186
 187   public static String getPDBIdwithSpecifiedChain(String pdbId,
 188           String searchTerm)
 189   {
 190     String pdbIdWithChainCode = "";
 191     if (searchTerm.contains(";"))
 192     {
 193       String[] foundTerms = searchTerm.split(";");
 194       for (String foundTerm : foundTerms)
 195       {
 196         if (foundTerm.contains(pdbId))
 197         {
 198           pdbIdWithChainCode = foundTerm;
 199         }
 200       }
 201     }
 202     else if (searchTerm.contains(pdbId))
 203     {
 204       pdbIdWithChainCode = searchTerm;
 205     }
 206     else
 207     {
 208       pdbIdWithChainCode = pdbId;
 209     }
 210     return pdbIdWithChainCode;
 211   }
 212
 213   /**
 214    * Populates search target combo-box options
 215    */
 216   public void populateCmbSearchTargetOptions()
 217   {
 218     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 219     searchableTargets.add(PDBDocField.PDB_ID);
 220     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 221     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 222     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 223     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 224     searchableTargets.add(PDBDocField.GENE_NAME);
 225     searchableTargets.add(PDBDocField.GENUS);
 226     searchableTargets.add(PDBDocField.ALL);
 227
 228     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 229     {
 230       @Override
 231       public int compare(PDBDocField o1, PDBDocField o2)
 232       {
 233         return o1.getName().compareTo(o2.getName());
 234       }
 235     });
 236
 237     for (PDBDocField searchTarget : searchableTargets)
 238     {
 239       cmb_searchTarget.addItem(searchTarget);
 240     }
 241   }
 242
 243 }