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.uimodel.PDBSearchRequest;
  10 import jalview.ws.uimodel.PDBSearchResponse;
  11 import jalview.ws.uimodel.PDBSummaryListModel;
  12 import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
  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 import javax.swing.SwingUtilities;
  21
  22 @SuppressWarnings("serial")
  23 public class StructureChooser extends GStructureChooser
  24 {
  25
  26
  27   private SequenceI sequence;
  28
  29
  30   public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
  31   {
  32     this.ap = ap;
  33     this.sequence = sequence;
  34     fetchStructures();
  35   }
  36
  37   @Override
  38   public void ok_ActionPerformed()
  39   {
  40     jListFoundStructures.setSelectedValue("op1x", true);
  41   }
  42
  43   public void pdbFromFile_actionPerformed()
  44   {
  45     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
  46             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
  47     chooser.setFileView(new jalview.io.JalviewFileView());
  48     chooser.setDialogTitle(MessageManager.formatMessage(
  49             "label.select_pdb_file_for", new String[]
  50             { sequence.getDisplayId(false) }));
  51     chooser.setToolTipText(MessageManager.formatMessage(
  52             "label.load_pdb_file_associate_with_sequence", new String[]
  53             { sequence.getDisplayId(false) }));
  54
  55     int value = chooser.showOpenDialog(null);
  56
  57     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
  58     {
  59       String choice = chooser.getSelectedFile().getPath();
  60       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
  61       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
  62               jalview.io.AppletFormatAdapter.FILE, sequence, true,
  63               Desktop.instance);
  64     }
  65
  66   }
  67
  68   public void discoverPDB_actionPerformed()
  69   {
  70
  71     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
  72     { sequence }
  73             : ap.av.getSequenceSelection());
  74     Thread discpdb = new Thread(new Runnable()
  75     {
  76       @Override
  77       public void run()
  78       {
  79
  80         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
  81                 .fetchDBRefs(false);
  82       }
  83
  84     });
  85     discpdb.start();
  86   }
  87
  88   // rpdbview.addActionListener(new ActionListener()
  89   // {
  90   //
  91   // @Override
  92   // public void actionPerformed(ActionEvent e)
  93   // {
  94   // new StructureViewer(ap.getStructureSelectionManager())
  95   // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
  96   // }
  97   // });
  98
  99   public void enterPDB_actionPerformed()
 100   {
 101     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
 102             MessageManager.getString("label.enter_pdb_id"),
 103             MessageManager.getString("label.enter_pdb_id"),
 104             JOptionPane.QUESTION_MESSAGE);
 105     if (id != null && id.length() > 0)
 106     {
 107       PDBEntry entry = new PDBEntry();
 108       entry.setId(id.toUpperCase());
 109       sequence.getDatasetSequence().addPDBId(entry);
 110     }
 111   }
 112
 113   public static void main(String[] args)
 114   {
 115     SwingUtilities.invokeLater(new Runnable()
 116     {
 117       public void run()
 118       {
 119         new StructureChooser(null, null);
 120       }
 121     });
 122   }
 123
 124   @SuppressWarnings("unchecked")
 125   protected void populateFilterOptions()
 126   {
 127     filterOptions.addItem(new FilterOptions("- Filter Criteria -", "",
 128             VIEWS_AUTO));
 129     filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO));
 130     filterOptions
 131             .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO));
 132     filterOptions.addItem(new FilterOptions("Best Resolution", "",
 133             VIEWS_AUTO));
 134     filterOptions
 135             .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO));
 136     filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID));
 137     filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE));
 138   }
 139
 140   protected void updateCurrentView()
 141   {
 142     String currentView = ((FilterOptions) filterOptions.getSelectedItem())
 143             .getView();
 144     switchableViewsLayout.show(switchableViewsPanel, currentView);
 145   }
 146
 147   private void fetchStructures()
 148   {
 149     long startTime = System.currentTimeMillis();
 150     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
 151     { sequence }
 152             : ap.av.getSequenceSelection());
 153     int foundStructures = 0;
 154     PDBSearchRequest request = new PDBSearchRequest();
 155     request.setAllowEmptySeq(false);
 156     request.setResponseSize(500);
 157     request.setSearchTarget("(text:");
 158     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 159     wantedFields.add(PDBDocField.MOLECULE_TYPE);
 160     wantedFields.add(PDBDocField.PDB_ID);
 161     wantedFields.add(PDBDocField.GENUS);
 162     wantedFields.add(PDBDocField.GENE_NAME);
 163     wantedFields.add(PDBDocField.TITLE);
 164     request.setWantedFields(wantedFields);
 165
 166     Collection<PDBSummaryListModel> searchSummaries = new HashSet<PDBSummaryListModel>();
 167     // searchSummaries.
 168     for (SequenceI seq : sequences)
 169     {
 170       // System.out.println("Selected : " + seq.getName());
 171       request.setSearchTerm(buildQuery(seq) + ")");
 172
 173       PDBRestClient pdbRestCleint = new PDBRestClient();
 174
 175       PDBSearchResponse resultList = pdbRestCleint
 176               .executeRequest(request);
 177       if (resultList.getSearchSummary() != null
 178               && !resultList.getSearchSummary().isEmpty())
 179       {
 180         searchSummaries.addAll(resultList.getSearchSummary());
 181       }
 182     }
 183
 184     foundStructures = searchSummaries.size();
 185     if (searchSummaries != null)
 186     {
 187       jListFoundStructures.setModel(PDBSearchResponse
 188               .getListModel(searchSummaries));
 189     }
 190
 191     String totalTime = (System.currentTimeMillis() - startTime)
 192             + " milli secs";
 193     mainFrame.setTitle("Structure Chooser - " + foundStructures
 194             + " Found (" + totalTime + ")");
 195   }
 196
 197   private String buildQuery(SequenceI seq)
 198   {
 199     String query = seq.getName();
 200     StringBuilder queryBuilder = new StringBuilder();
 201     int count = 0;
 202     if (seq.getDBRef() != null && seq.getDBRef().length != 0)
 203     {
 204       for (DBRefEntry dbRef : seq.getDBRef())
 205       {
 206         System.out.println("dbref : " + dbRef.getAccessionId());
 207         queryBuilder.append("text:").append(dbRef.getAccessionId())
 208                 .append(" OR ");
 209         ++count;
 210         if (count > 10)
 211         {
 212           break;
 213         }
 214       }
 215       // int beginIndex = queryBuilder. firstIndexOf("text");
 216       int endIndex = queryBuilder.lastIndexOf(" OR ");
 217       query = queryBuilder.toString().substring(5, endIndex);
 218     }
 219     System.out.println("------------> " + query);
 220     return query;
 221   }
 222
 223   public class FilterOptions
 224   {
 225     private String name;
 226
 227     private String value;
 228
 229     private String view;
 230
 231     public FilterOptions(String name, String value, String view)
 232     {
 233       this.name = name;
 234       this.value = value;
 235       this.view = view;
 236     }
 237
 238     public String getName()
 239     {
 240       return name;
 241     }
 242
 243     public void setName(String name)
 244     {
 245       this.name = name;
 246     }
 247
 248     public String getValue()
 249     {
 250       return value;
 251     }
 252
 253     public void setValue(String value)
 254     {
 255       this.value = value;
 256     }
 257
 258     public String getView()
 259     {
 260       return view;
 261     }
 262
 263     public void setView(String view)
 264     {
 265       this.view = view;
 266     }
 267
 268     public String toString()
 269     {
 270       return this.name;
 271     }
 272   }
 273 }