src/jalview/gui/StructureChooser.java

   1 package jalview.gui;
   2
   3 import jalview.datamodel.DBRefEntry;
   4 import jalview.datamodel.PDBEntry;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.jbgui.GStructureChooser;
   7 import jalview.util.MessageManager;
   8 import jalview.ws.dbsources.PDBRestClient;
   9 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
  10 import jalview.ws.uimodel.PDBSearchRequest;
  11 import jalview.ws.uimodel.PDBSearchResponse;
  12 import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
  13
  14 import java.awt.Component;
  15 import java.awt.event.ItemEvent;
  16 import java.util.ArrayList;
  17 import java.util.Collection;
  18 import java.util.HashSet;
  19 import java.util.List;
  20
  21 import javax.swing.JCheckBox;
  22 import javax.swing.JOptionPane;
  23 import javax.swing.JTable;
  24 import javax.swing.ListSelectionModel;
  25 import javax.swing.table.TableCellRenderer;
  26 import javax.swing.table.TableColumnModel;
  27
  28 @SuppressWarnings("serial")
  29 public class StructureChooser extends GStructureChooser
  30 {
  31
  32   private boolean structuresWereFound = false;
  33
  34   private SequenceI selectedSequence;
  35
  36   private SequenceI[] selectedSequences;
  37
  38   IProgressIndicator af;
  39
  40   Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
  41
  42   public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
  43   {
  44     this.ap = ap;
  45     this.af = ap.alignFrame;
  46     this.selectedSequence = sequence;
  47     this.selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
  48     { sequence }
  49             : ap.av.getSequenceSelection());
  50     init();
  51   }
  52
  53   private void init()
  54   {
  55     Thread discPDBThread = new Thread(new Runnable()
  56     {
  57       @Override
  58       public void run()
  59       {
  60         long startTime = System.currentTimeMillis();
  61         af.setProgressBar(
  62                 MessageManager.getString("status.fetching_db_refs"),
  63                 startTime);
  64
  65         fetchStructures();
  66         populateFilterOptions();
  67         af.setProgressBar(null, startTime);
  68         mainFrame.setVisible(true);
  69         updateCurrentView();
  70       }
  71     });
  72     discPDBThread.start();
  73   }
  74
  75   private void fetchStructures()
  76   {
  77     long startTime = System.currentTimeMillis();
  78     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  79     // wantedFields.add(PDBDocField.MOLECULE_TYPE);
  80     wantedFields.add(PDBDocField.PDB_ID);
  81     // wantedFields.add(PDBDocField.GENUS);
  82     // wantedFields.add(PDBDocField.GENE_NAME);
  83     wantedFields.add(PDBDocField.TITLE);
  84
  85     PDBSearchRequest request = new PDBSearchRequest();
  86     request.setAllowEmptySeq(false);
  87     request.setResponseSize(500);
  88     request.setFieldToSearchBy("(text:");
  89     request.setWantedFields(wantedFields);
  90
  91     for (SequenceI seq : selectedSequences)
  92     {
  93       request.setSearchTerm(buildQuery(seq) + ")");
  94       request.setAssociatedSequence(seq.getName());
  95       PDBRestClient pdbRestCleint = new PDBRestClient();
  96       PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
  97       if (resultList.getSearchSummary() != null
  98               && !resultList.getSearchSummary().isEmpty())
  99       {
 100         discoveredStructuresSet.addAll(resultList.getSearchSummary());
 101       }
 102     }
 103
 104     int noOfStructuresFound = 0;
 105     if (discoveredStructuresSet != null)
 106     {
 107       jListFoundStructures.setModel(PDBSearchResponse
 108               .getListModel(discoveredStructuresSet));
 109       summaryTable.setModel(PDBSearchResponse.getTableModel(request,
 110               discoveredStructuresSet));
 111       // resizeColumnWidth(summaryTable);
 112       structuresWereFound = true;
 113       noOfStructuresFound = discoveredStructuresSet.size();
 114     }
 115     String totalTime = (System.currentTimeMillis() - startTime)
 116             + " milli secs";
 117     mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
 118             + " Found (" + totalTime + ")");
 119   }
 120
 121   public void resizeColumnWidth(JTable table)
 122   {
 123     // table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
 124     final TableColumnModel columnModel = table.getColumnModel();
 125     for (int column = 0; column < table.getColumnCount(); column++)
 126     {
 127       int width = 50; // Min width
 128       for (int row = 0; row < table.getRowCount(); row++)
 129       {
 130         TableCellRenderer renderer = table.getCellRenderer(row, column);
 131         Component comp = table.prepareRenderer(renderer, row, column);
 132         width = Math.max(comp.getPreferredSize().width, width);
 133       }
 134       columnModel.getColumn(column).setPreferredWidth(width);
 135     }
 136   }
 137
 138   protected void populateFilterOptions()
 139   {
 140     if (structuresWereFound)
 141     {
 142       filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
 143               PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
 144       filterOptionsComboBox.addItem(new FilterOptions(
 145               "Best UniProt Coverage", PDBDocField.UNIPROT_COVERAGE
 146                       .getCode(), VIEWS_FILTER));
 147       filterOptionsComboBox.addItem(new FilterOptions("Highest Resolution",
 148               PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
 149       filterOptionsComboBox.addItem(new FilterOptions(
 150               "Highest Protein Chain", PDBDocField.PROTEIN_CHAIN_COUNT
 151                       .getCode(), VIEWS_FILTER));
 152       filterOptionsComboBox.addItem(new FilterOptions(
 153               "Highest Bound Molecules", PDBDocField.BOUND_MOLECULE_COUNT
 154                       .getCode(), VIEWS_FILTER));
 155       filterOptionsComboBox.addItem(new FilterOptions(
 156               "Highest Polymer Residues", PDBDocField.POLYMER_RESIDUE_COUNT
 157                       .getCode(), VIEWS_FILTER));
 158     }
 159     filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
 160             VIEWS_ENTER_ID));
 161     filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
 162             VIEWS_FROM_FILE));
 163   }
 164
 165   private String buildQuery(SequenceI seq)
 166   {
 167     String query = seq.getName();
 168     StringBuilder queryBuilder = new StringBuilder();
 169     int count = 0;
 170     if (seq.getDBRef() != null && seq.getDBRef().length != 0)
 171     {
 172       for (DBRefEntry dbRef : seq.getDBRef())
 173       {
 174         queryBuilder.append("text:").append(dbRef.getAccessionId())
 175                 .append(" OR ");
 176         ++count;
 177         if (count > 10)
 178         {
 179           break;
 180         }
 181       }
 182       int endIndex = queryBuilder.lastIndexOf(" OR ");
 183       query = queryBuilder.toString().substring(5, endIndex);
 184     }
 185     return query;
 186   }
 187
 188   protected void updateCurrentView()
 189   {
 190     FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
 191             .getSelectedItem());
 192     switchableViewsLayout.show(switchableViewsPanel,
 193             currentOption.getView());
 194     invertFilter.setEnabled(false);
 195     if (currentOption.getView() == VIEWS_FILTER)
 196     {
 197       invertFilter.setEnabled(true);
 198       filterResultSet(currentOption.getValue());
 199     }
 200   }
 201
 202   public void filterResultSet(final String fieldToFilterBy)
 203   {
 204     Thread filterThread = new Thread(new Runnable()
 205     {
 206       @Override
 207       public void run()
 208       {
 209         try
 210         {
 211         loadingImageLabel.setVisible(true);
 212         List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 213         // wantedFields.add(PDBDocField.MOLECULE_TYPE);
 214         wantedFields.add(PDBDocField.PDB_ID);
 215         // wantedFields.add(PDBDocField.GENUS);
 216         // wantedFields.add(PDBDocField.GENE_NAME);
 217         wantedFields.add(PDBDocField.TITLE);
 218
 219         PDBSearchRequest request = new PDBSearchRequest();
 220         request.setAllowEmptySeq(false);
 221         request.setResponseSize(1);
 222         request.setFieldToSearchBy("(text:");
 223         request.setFieldToSortBy(fieldToFilterBy,
 224                 !invertFilter.isSelected());
 225
 226         request.setWantedFields(wantedFields);
 227
 228         Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
 229         for (SequenceI seq : selectedSequences)
 230         {
 231           request.setSearchTerm(buildQuery(seq) + ")");
 232           request.setAssociatedSequence(seq.getName());
 233           PDBRestClient pdbRestCleint = new PDBRestClient();
 234           PDBSearchResponse resultList = pdbRestCleint
 235                   .executeRequest(request);
 236           if (resultList.getSearchSummary() != null
 237                   && !resultList.getSearchSummary().isEmpty())
 238           {
 239             filteredResponse.addAll(resultList.getSearchSummary());
 240           }
 241         }
 242
 243
 244         if (filteredResponse != null)
 245         {
 246             //
 247             // for (PDBResponseSummary s : filteredResponse)
 248             // {
 249             // System.out.println("-----------> " + s.getPdbId());
 250             // }
 251
 252           int filterResponseCount = filteredResponse.size();
 253           List<PDBResponseSummary> list = new ArrayList<PDBResponseSummary>(
 254                   discoveredStructuresSet);
 255           list.removeAll(filteredResponse);
 256
 257           Collection<PDBResponseSummary> newSet = new ArrayList<PDBResponseSummary>();
 258           newSet.addAll(filteredResponse);
 259           newSet.addAll(list);
 260
 261           jListFoundStructures.setModel(PDBSearchResponse
 262                   .getListModel(newSet));
 263           summaryTable.setModel(PDBSearchResponse.getTableModel(request,
 264                   newSet));
 265           // resizeColumnWidth(summaryTable);
 266           list = null;
 267           newSet = null;
 268
 269           int[] filterIndice = new int[filterResponseCount];
 270           ListSelectionModel model = summaryTable.getSelectionModel();
 271           model.clearSelection();
 272           // int x = 0;
 273           for (int x = 0; x < filterResponseCount; x++)
 274           {
 275             filterIndice[x] = x;
 276             model.addSelectionInterval(x, x);
 277           }
 278           jListFoundStructures.setSelectedIndices(filterIndice);
 279         }
 280
 281         loadingImageLabel.setVisible(false);
 282         } catch (Exception e)
 283         {
 284           e.printStackTrace();
 285         }
 286       }
 287     });
 288     filterThread.start();
 289
 290   }
 291
 292   @Override
 293   protected void stateChanged(ItemEvent e)
 294   {
 295     if (e.getSource() instanceof JCheckBox)
 296     {
 297       updateCurrentView();
 298     }
 299     else
 300     {
 301       if (e.getStateChange() == ItemEvent.SELECTED)
 302       {
 303         updateCurrentView();
 304       }
 305     }
 306
 307   }
 308
 309   @Override
 310   public void ok_ActionPerformed()
 311   {
 312     // TODO code to load selected structures to jmol or chimera
 313   }
 314
 315   public void pdbFromFile_actionPerformed()
 316   {
 317     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 318             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 319     chooser.setFileView(new jalview.io.JalviewFileView());
 320     chooser.setDialogTitle(MessageManager.formatMessage(
 321             "label.select_pdb_file_for", new String[]
 322             { selectedSequence.getDisplayId(false) }));
 323     chooser.setToolTipText(MessageManager.formatMessage(
 324             "label.load_pdb_file_associate_with_sequence", new String[]
 325             { selectedSequence.getDisplayId(false) }));
 326
 327     int value = chooser.showOpenDialog(null);
 328
 329     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 330     {
 331       String choice = chooser.getSelectedFile().getPath();
 332       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
 333       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
 334               jalview.io.AppletFormatAdapter.FILE, selectedSequence, true,
 335               Desktop.instance);
 336     }
 337
 338   }
 339
 340   // rpdbview.addActionListener(new ActionListener()
 341   // {
 342   //
 343   // @Override
 344   // public void actionPerformed(ActionEvent e)
 345   // {
 346   // new StructureViewer(ap.getStructureSelectionManager())
 347   // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
 348   // }
 349   // });
 350
 351   public void enterPDB_actionPerformed()
 352   {
 353     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
 354             MessageManager.getString("label.enter_pdb_id"),
 355             MessageManager.getString("label.enter_pdb_id"),
 356             JOptionPane.QUESTION_MESSAGE);
 357     if (id != null && id.length() > 0)
 358     {
 359       PDBEntry entry = new PDBEntry();
 360       entry.setId(id.toUpperCase());
 361       selectedSequence.getDatasetSequence().addPDBId(entry);
 362     }
 363   }
 364
 365 }