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.util.ArrayList;
  15 import java.util.Collection;
  16 import java.util.HashSet;
  17 import java.util.List;
  18
  19 import javax.swing.JOptionPane;
  20
  21 @SuppressWarnings("serial")
  22 public class StructureChooser extends GStructureChooser
  23 {
  24
  25   private boolean structuresWereFound = false;
  26
  27   private SequenceI selectedSequence;
  28
  29   private SequenceI[] selectedSequences;
  30
  31   public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
  32   {
  33     this.ap = ap;
  34     this.selectedSequence = sequence;
  35     selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
  36     { sequence } : ap.av.getSequenceSelection());
  37     fetchStructures();
  38     populateFilterOptions();
  39     updateCurrentView();
  40   }
  41
  42   @Override
  43   public void ok_ActionPerformed()
  44   {
  45     // TODO code to load selected structures to jmol or chimera
  46   }
  47
  48   protected void populateFilterOptions()
  49   {
  50     if (structuresWereFound)
  51     {
  52       filterOptionsComboBox.addItem(new FilterOptions(
  53               "- Filter Criteria -", "",
  54               VIEWS_FILTER));
  55       filterOptionsComboBox.addItem(new FilterOptions("All", "all",
  56               VIEWS_FILTER));
  57       filterOptionsComboBox.addItem(new FilterOptions("Best Coverage",
  58               "coverage",
  59               VIEWS_FILTER));
  60       filterOptionsComboBox.addItem(new FilterOptions("Best Resolution",
  61               PDBDocField.RESOLUTION.getCode(),
  62               VIEWS_FILTER));
  63       filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
  64               PDBDocField.OVERALL_QUALITY.getCode(),
  65               VIEWS_FILTER));
  66
  67       // "number_of_polymers"), PROTEIN_CHAIN_COUNT(
  68       // "Protein Chain Count", "number_of_protein_chains"),
  69       // BOUND_MOLECULE_COUNT(
  70       // "Bound Molecule Count", "number_of_bound_molecules"),
  71       // POLYMER_RESIDUE_COUNT(
  72       // "Polymer Residue Count", "number_of_polymer_residues"),
  73       // UNIPROT_COVERAGE(
  74     }
  75     filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
  76             VIEWS_ENTER_ID));
  77     filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
  78             VIEWS_FROM_FILE));
  79   }
  80
  81   private void fetchStructures()
  82   {
  83     long startTime = System.currentTimeMillis();
  84     // final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new
  85     // SequenceI[]
  86     // { sequence }
  87     // : ap.av.getSequenceSelection());
  88
  89     int foundStructures = 0;
  90     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  91     wantedFields.add(PDBDocField.MOLECULE_TYPE);
  92     wantedFields.add(PDBDocField.PDB_ID);
  93     wantedFields.add(PDBDocField.GENUS);
  94     wantedFields.add(PDBDocField.GENE_NAME);
  95     wantedFields.add(PDBDocField.TITLE);
  96
  97     PDBSearchRequest request = new PDBSearchRequest();
  98     request.setAllowEmptySeq(false);
  99     request.setResponseSize(500);
 100     request.setSearchTarget("(text:");
 101     request.setWantedFields(wantedFields);
 102
 103     Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
 104     for (SequenceI seq : selectedSequences)
 105     {
 106       request.setSearchTerm(buildQuery(seq) + ")");
 107       PDBRestClient pdbRestCleint = new PDBRestClient();
 108       PDBSearchResponse resultList = pdbRestCleint
 109               .executeRequest(request);
 110       if (resultList.getSearchSummary() != null
 111               && !resultList.getSearchSummary().isEmpty())
 112       {
 113         searchSummaries.addAll(resultList.getSearchSummary());
 114       }
 115     }
 116
 117     foundStructures = searchSummaries.size();
 118     if (searchSummaries != null)
 119     {
 120       jListFoundStructures.setModel(PDBSearchResponse
 121               .getListModel(searchSummaries));
 122       structuresWereFound = true;
 123     }
 124     String totalTime = (System.currentTimeMillis() - startTime)
 125             + " milli secs";
 126     mainFrame.setTitle("Structure Chooser - " + foundStructures
 127             + " Found (" + totalTime + ")");
 128   }
 129
 130   private String buildQuery(SequenceI seq)
 131   {
 132     String query = seq.getName();
 133     StringBuilder queryBuilder = new StringBuilder();
 134     int count = 0;
 135     if (seq.getDBRef() != null && seq.getDBRef().length != 0)
 136     {
 137       for (DBRefEntry dbRef : seq.getDBRef())
 138       {
 139         queryBuilder.append("text:").append(dbRef.getAccessionId())
 140                 .append(" OR ");
 141         ++count;
 142         if (count > 10)
 143         {
 144           break;
 145         }
 146       }
 147       int endIndex = queryBuilder.lastIndexOf(" OR ");
 148       query = queryBuilder.toString().substring(5, endIndex);
 149     }
 150     return query;
 151   }
 152
 153   @Override
 154   protected void stateChanged()
 155   {
 156     updateCurrentView();
 157   }
 158
 159   int debounceCount = 0;
 160   protected void updateCurrentView()
 161   {
 162     FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
 163             .getSelectedItem());
 164     switchableViewsLayout.show(switchableViewsPanel,
 165             currentOption.getView());
 166     ++debounceCount;
 167     if (currentOption.getView() == VIEWS_FILTER && debounceCount % 2 == 0)
 168     {
 169       filterResultSet(currentOption.getValue());
 170     }
 171   }
 172
 173   public void filterResultSet(String filterTarget)
 174   {
 175     System.out.println("-----------------> Filter by : " + filterTarget);
 176
 177     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 178     wantedFields.add(PDBDocField.MOLECULE_TYPE);
 179     wantedFields.add(PDBDocField.PDB_ID);
 180     wantedFields.add(PDBDocField.GENUS);
 181     wantedFields.add(PDBDocField.GENE_NAME);
 182     wantedFields.add(PDBDocField.TITLE);
 183
 184     PDBSearchRequest request = new PDBSearchRequest();
 185     request.setAllowEmptySeq(false);
 186     request.setResponseSize(1);
 187     request.setSearchTarget("(text:");
 188     request.setSortTarget(filterTarget, true);
 189
 190     request.setWantedFields(wantedFields);
 191
 192     Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
 193     for (SequenceI seq : selectedSequences)
 194     {
 195       request.setSearchTerm(buildQuery(seq) + ")");
 196       PDBRestClient pdbRestCleint = new PDBRestClient();
 197       PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
 198       if (resultList.getSearchSummary() != null
 199               && !resultList.getSearchSummary().isEmpty())
 200       {
 201         searchSummaries.addAll(resultList.getSearchSummary());
 202
 203       }
 204     }
 205
 206     for (PDBResponseSummary summary : searchSummaries)
 207     {
 208       jListFoundStructures.setSelectedValue(summary, true);
 209       // jListFoundStructures.
 210       break;
 211     }
 212     System.out.println("Found item count : " + searchSummaries.size());
 213   }
 214
 215   public void pdbFromFile_actionPerformed()
 216   {
 217     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
 218             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 219     chooser.setFileView(new jalview.io.JalviewFileView());
 220     chooser.setDialogTitle(MessageManager.formatMessage(
 221             "label.select_pdb_file_for", new String[]
 222             { selectedSequence.getDisplayId(false) }));
 223     chooser.setToolTipText(MessageManager.formatMessage(
 224             "label.load_pdb_file_associate_with_sequence", new String[]
 225             { selectedSequence.getDisplayId(false) }));
 226
 227     int value = chooser.showOpenDialog(null);
 228
 229     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
 230     {
 231       String choice = chooser.getSelectedFile().getPath();
 232       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
 233       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
 234               jalview.io.AppletFormatAdapter.FILE, selectedSequence, true,
 235               Desktop.instance);
 236     }
 237
 238   }
 239
 240
 241   // rpdbview.addActionListener(new ActionListener()
 242   // {
 243   //
 244   // @Override
 245   // public void actionPerformed(ActionEvent e)
 246   // {
 247   // new StructureViewer(ap.getStructureSelectionManager())
 248   // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
 249   // }
 250   // });
 251
 252   public void enterPDB_actionPerformed()
 253   {
 254     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
 255             MessageManager.getString("label.enter_pdb_id"),
 256             MessageManager.getString("label.enter_pdb_id"),
 257             JOptionPane.QUESTION_MESSAGE);
 258     if (id != null && id.length() > 0)
 259     {
 260       PDBEntry entry = new PDBEntry();
 261       entry.setId(id.toUpperCase());
 262       selectedSequence.getDatasetSequence().addPDBId(entry);
 263     }
 264   }
 265
 266   // public static void main(String[] args)
 267   // {
 268   // SwingUtilities.invokeLater(new Runnable()
 269   // {
 270   // public void run()
 271   // {
 272   // new StructureChooser(null, null);
 273   // }
 274   // });
 275   // }
 276
 277
 278 }