import jalview.jbgui.GStructureChooser;
import jalview.util.MessageManager;
import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import jalview.ws.uimodel.PDBSearchRequest;
import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSummaryListModel;
-import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
+import java.awt.Component;
+import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
+import javax.swing.JCheckBox;
import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumnModel;
@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
{
+ private boolean structuresWereFound = false;
- private SequenceI sequence;
+ private SequenceI selectedSequence;
+ private SequenceI[] selectedSequences;
- public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
- {
- this.ap = ap;
- this.sequence = sequence;
- fetchStructures();
- }
+ IProgressIndicator af;
- @Override
- public void ok_ActionPerformed()
- {
- jListFoundStructures.setSelectedValue("op1x", true);
- }
+ Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
- public void pdbFromFile_actionPerformed()
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for", new String[]
- { sequence.getDisplayId(false) }));
- chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new String[]
- { sequence.getDisplayId(false) }));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
- jalview.io.AppletFormatAdapter.FILE, sequence, true,
- Desktop.instance);
- }
-
- }
-
- public void discoverPDB_actionPerformed()
+ public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
{
-
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
+ this.ap = ap;
+ this.af = ap.alignFrame;
+ this.selectedSequence = sequence;
+ this.selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
{ sequence }
: ap.av.getSequenceSelection());
- Thread discpdb = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
-
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
- .fetchDBRefs(false);
- }
-
- });
- discpdb.start();
+ init();
}
- // rpdbview.addActionListener(new ActionListener()
- // {
- //
- // @Override
- // public void actionPerformed(ActionEvent e)
- // {
- // new StructureViewer(ap.getStructureSelectionManager())
- // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- // }
- // });
-
- public void enterPDB_actionPerformed()
- {
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"),
- MessageManager.getString("label.enter_pdb_id"),
- JOptionPane.QUESTION_MESSAGE);
- if (id != null && id.length() > 0)
- {
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- sequence.getDatasetSequence().addPDBId(entry);
- }
- }
-
- public static void main(String[] args)
+ private void init()
{
- SwingUtilities.invokeLater(new Runnable()
+ Thread discPDBThread = new Thread(new Runnable()
{
+ @Override
public void run()
{
- new StructureChooser(null, null);
+ long startTime = System.currentTimeMillis();
+ af.setProgressBar(
+ MessageManager.getString("status.fetching_db_refs"),
+ startTime);
+
+ fetchStructures();
+ populateFilterOptions();
+ af.setProgressBar(null, startTime);
+ mainFrame.setVisible(true);
+ updateCurrentView();
}
});
- }
-
- @SuppressWarnings("unchecked")
- protected void populateFilterOptions()
- {
- filterOptions.addItem(new FilterOptions("- Filter Criteria -", "",
- VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO));
- filterOptions
- .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("Best Resolution", "",
- VIEWS_AUTO));
- filterOptions
- .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO));
- filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID));
- filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE));
- }
-
- protected void updateCurrentView()
- {
- String currentView = ((FilterOptions) filterOptions.getSelectedItem())
- .getView();
- switchableViewsLayout.show(switchableViewsPanel, currentView);
+ discPDBThread.start();
}
private void fetchStructures()
{
long startTime = System.currentTimeMillis();
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
- int foundStructures = 0;
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(500);
- request.setSearchTarget("(text:");
List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ // wantedFields.add(PDBDocField.MOLECULE_TYPE);
wantedFields.add(PDBDocField.PDB_ID);
- wantedFields.add(PDBDocField.GENUS);
- wantedFields.add(PDBDocField.GENE_NAME);
+ // wantedFields.add(PDBDocField.GENUS);
+ // wantedFields.add(PDBDocField.GENE_NAME);
wantedFields.add(PDBDocField.TITLE);
+
+ PDBSearchRequest request = new PDBSearchRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(500);
+ request.setFieldToSearchBy("(text:");
request.setWantedFields(wantedFields);
-
- Collection<PDBSummaryListModel> searchSummaries = new HashSet<PDBSummaryListModel>();
- // searchSummaries.
- for (SequenceI seq : sequences)
+
+ for (SequenceI seq : selectedSequences)
{
- // System.out.println("Selected : " + seq.getName());
request.setSearchTerm(buildQuery(seq) + ")");
-
+ request.setAssociatedSequence(seq.getName());
PDBRestClient pdbRestCleint = new PDBRestClient();
-
- PDBSearchResponse resultList = pdbRestCleint
- .executeRequest(request);
+ PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
- searchSummaries.addAll(resultList.getSearchSummary());
+ discoveredStructuresSet.addAll(resultList.getSearchSummary());
}
}
- foundStructures = searchSummaries.size();
- if (searchSummaries != null)
+ int noOfStructuresFound = 0;
+ if (discoveredStructuresSet != null)
{
jListFoundStructures.setModel(PDBSearchResponse
- .getListModel(searchSummaries));
+ .getListModel(discoveredStructuresSet));
+ summaryTable.setModel(PDBSearchResponse.getTableModel(request,
+ discoveredStructuresSet));
+ // resizeColumnWidth(summaryTable);
+ structuresWereFound = true;
+ noOfStructuresFound = discoveredStructuresSet.size();
}
-
String totalTime = (System.currentTimeMillis() - startTime)
+ " milli secs";
- mainFrame.setTitle("Structure Chooser - " + foundStructures
+ mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+ " Found (" + totalTime + ")");
}
+ public void resizeColumnWidth(JTable table)
+ {
+ // table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
+ final TableColumnModel columnModel = table.getColumnModel();
+ for (int column = 0; column < table.getColumnCount(); column++)
+ {
+ int width = 50; // Min width
+ for (int row = 0; row < table.getRowCount(); row++)
+ {
+ TableCellRenderer renderer = table.getCellRenderer(row, column);
+ Component comp = table.prepareRenderer(renderer, row, column);
+ width = Math.max(comp.getPreferredSize().width, width);
+ }
+ columnModel.getColumn(column).setPreferredWidth(width);
+ }
+ }
+
+ protected void populateFilterOptions()
+ {
+ if (structuresWereFound)
+ {
+ filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
+ PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
+ filterOptionsComboBox.addItem(new FilterOptions(
+ "Best UniProt Coverage", PDBDocField.UNIPROT_COVERAGE
+ .getCode(), VIEWS_FILTER));
+ filterOptionsComboBox.addItem(new FilterOptions("Highest Resolution",
+ PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+ filterOptionsComboBox.addItem(new FilterOptions(
+ "Highest Protein Chain", PDBDocField.PROTEIN_CHAIN_COUNT
+ .getCode(), VIEWS_FILTER));
+ filterOptionsComboBox.addItem(new FilterOptions(
+ "Highest Bound Molecules", PDBDocField.BOUND_MOLECULE_COUNT
+ .getCode(), VIEWS_FILTER));
+ filterOptionsComboBox.addItem(new FilterOptions(
+ "Highest Polymer Residues", PDBDocField.POLYMER_RESIDUE_COUNT
+ .getCode(), VIEWS_FILTER));
+ }
+ filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
+ VIEWS_ENTER_ID));
+ filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
+ VIEWS_FROM_FILE));
+ }
+
private String buildQuery(SequenceI seq)
{
String query = seq.getName();
{
for (DBRefEntry dbRef : seq.getDBRef())
{
- System.out.println("dbref : " + dbRef.getAccessionId());
queryBuilder.append("text:").append(dbRef.getAccessionId())
.append(" OR ");
++count;
break;
}
}
- // int beginIndex = queryBuilder. firstIndexOf("text");
int endIndex = queryBuilder.lastIndexOf(" OR ");
query = queryBuilder.toString().substring(5, endIndex);
}
- System.out.println("------------> " + query);
return query;
}
- public class FilterOptions
+ protected void updateCurrentView()
{
- private String name;
-
- private String value;
-
- private String view;
-
- public FilterOptions(String name, String value, String view)
+ FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
+ .getSelectedItem());
+ switchableViewsLayout.show(switchableViewsPanel,
+ currentOption.getView());
+ invertFilter.setEnabled(false);
+ if (currentOption.getView() == VIEWS_FILTER)
{
- this.name = name;
- this.value = value;
- this.view = view;
+ invertFilter.setEnabled(true);
+ filterResultSet(currentOption.getValue());
}
+ }
- public String getName()
+ public void filterResultSet(final String fieldToFilterBy)
+ {
+ Thread filterThread = new Thread(new Runnable()
{
- return name;
- }
+ @Override
+ public void run()
+ {
+ try
+ {
+ loadingImageLabel.setVisible(true);
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ // wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ // wantedFields.add(PDBDocField.GENUS);
+ // wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+
+ PDBSearchRequest request = new PDBSearchRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(1);
+ request.setFieldToSearchBy("(text:");
+ request.setFieldToSortBy(fieldToFilterBy,
+ !invertFilter.isSelected());
+
+ request.setWantedFields(wantedFields);
+
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ for (SequenceI seq : selectedSequences)
+ {
+ request.setSearchTerm(buildQuery(seq) + ")");
+ request.setAssociatedSequence(seq.getName());
+ PDBRestClient pdbRestCleint = new PDBRestClient();
+ PDBSearchResponse resultList = pdbRestCleint
+ .executeRequest(request);
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
- public void setName(String name)
- {
- this.name = name;
- }
- public String getValue()
- {
- return value;
- }
+ if (filteredResponse != null)
+ {
+ //
+ // for (PDBResponseSummary s : filteredResponse)
+ // {
+ // System.out.println("-----------> " + s.getPdbId());
+ // }
+
+ int filterResponseCount = filteredResponse.size();
+ List<PDBResponseSummary> list = new ArrayList<PDBResponseSummary>(
+ discoveredStructuresSet);
+ list.removeAll(filteredResponse);
+
+ Collection<PDBResponseSummary> newSet = new ArrayList<PDBResponseSummary>();
+ newSet.addAll(filteredResponse);
+ newSet.addAll(list);
+
+ jListFoundStructures.setModel(PDBSearchResponse
+ .getListModel(newSet));
+ summaryTable.setModel(PDBSearchResponse.getTableModel(request,
+ newSet));
+ // resizeColumnWidth(summaryTable);
+ list = null;
+ newSet = null;
+
+ int[] filterIndice = new int[filterResponseCount];
+ ListSelectionModel model = summaryTable.getSelectionModel();
+ model.clearSelection();
+ // int x = 0;
+ for (int x = 0; x < filterResponseCount; x++)
+ {
+ filterIndice[x] = x;
+ model.addSelectionInterval(x, x);
+ }
+ jListFoundStructures.setSelectedIndices(filterIndice);
+ }
+
+ loadingImageLabel.setVisible(false);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ });
+ filterThread.start();
+
+ }
- public void setValue(String value)
+ @Override
+ protected void stateChanged(ItemEvent e)
+ {
+ if (e.getSource() instanceof JCheckBox)
{
- this.value = value;
+ updateCurrentView();
}
-
- public String getView()
+ else
{
- return view;
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ updateCurrentView();
+ }
}
- public void setView(String view)
+ }
+
+ @Override
+ public void ok_ActionPerformed()
+ {
+ // TODO code to load selected structures to jmol or chimera
+ }
+
+ public void pdbFromFile_actionPerformed()
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { selectedSequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { selectedSequence.getDisplayId(false) }));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- this.view = view;
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
+ jalview.io.AppletFormatAdapter.FILE, selectedSequence, true,
+ Desktop.instance);
}
- public String toString()
+ }
+
+ // rpdbview.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // new StructureViewer(ap.getStructureSelectionManager())
+ // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
+ // }
+ // });
+
+ public void enterPDB_actionPerformed()
+ {
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
+ if (id != null && id.length() > 0)
{
- return this.name;
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id.toUpperCase());
+ selectedSequence.getDatasetSequence().addPDBId(entry);
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff