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