import jalview.ws.uimodel.PDBSearchResponse;
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.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumnModel;
@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
private SequenceI[] selectedSequences;
+ IProgressIndicator af;
+
+ Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+
public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
{
this.ap = ap;
+ this.af = ap.alignFrame;
this.selectedSequence = sequence;
- selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence } : ap.av.getSequenceSelection());
- fetchStructures();
- populateFilterOptions();
- updateCurrentView();
- }
-
- @Override
- public void ok_ActionPerformed()
- {
- // TODO code to load selected structures to jmol or chimera
+ this.selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
+ { sequence }
+ : ap.av.getSequenceSelection());
+ init();
}
- protected void populateFilterOptions()
+ private void init()
{
- if (structuresWereFound)
+ Thread discPDBThread = new Thread(new Runnable()
{
- filterOptionsComboBox.addItem(new FilterOptions(
- "- Filter Criteria -", "",
- VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions("All", "all",
- VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions("Best Coverage",
- "coverage",
- VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions("Best Resolution",
- PDBDocField.RESOLUTION.getCode(),
- VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
- PDBDocField.OVERALL_QUALITY.getCode(),
- VIEWS_FILTER));
-
- // "number_of_polymers"), PROTEIN_CHAIN_COUNT(
- // "Protein Chain Count", "number_of_protein_chains"),
- // BOUND_MOLECULE_COUNT(
- // "Bound Molecule Count", "number_of_bound_molecules"),
- // POLYMER_RESIDUE_COUNT(
- // "Polymer Residue Count", "number_of_polymer_residues"),
- // UNIPROT_COVERAGE(
- }
- filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
- filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
- VIEWS_FROM_FILE));
+ @Override
+ public void run()
+ {
+ long startTime = System.currentTimeMillis();
+ af.setProgressBar(
+ MessageManager.getString("status.fetching_db_refs"),
+ startTime);
+
+ fetchStructures();
+ populateFilterOptions();
+ af.setProgressBar(null, startTime);
+ mainFrame.setVisible(true);
+ updateCurrentView();
+ }
+ });
+ 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;
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.setSearchTarget("(text:");
+ request.setFieldToSearchBy("(text:");
request.setWantedFields(wantedFields);
-
- Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
+
for (SequenceI seq : selectedSequences)
{
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();
return query;
}
- @Override
- protected void stateChanged()
- {
- updateCurrentView();
- }
-
- int debounceCount = 0;
protected void updateCurrentView()
{
FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
.getSelectedItem());
switchableViewsLayout.show(switchableViewsPanel,
currentOption.getView());
- ++debounceCount;
- if (currentOption.getView() == VIEWS_FILTER && debounceCount % 2 == 0)
+ invertFilter.setEnabled(false);
+ if (currentOption.getView() == VIEWS_FILTER)
{
+ invertFilter.setEnabled(true);
filterResultSet(currentOption.getValue());
}
}
- public void filterResultSet(String filterTarget)
+ public void filterResultSet(final String fieldToFilterBy)
{
- System.out.println("-----------------> Filter by : " + filterTarget);
+ Thread filterThread = new Thread(new Runnable()
+ {
+ @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());
+ }
+ }
- 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.setSearchTarget("(text:");
- request.setSortTarget(filterTarget, true);
+ 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);
+ }
- request.setWantedFields(wantedFields);
+ loadingImageLabel.setVisible(false);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ });
+ filterThread.start();
- Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
- for (SequenceI seq : selectedSequences)
+ }
+
+ @Override
+ protected void stateChanged(ItemEvent e)
+ {
+ if (e.getSource() instanceof JCheckBox)
{
- request.setSearchTerm(buildQuery(seq) + ")");
- PDBRestClient pdbRestCleint = new PDBRestClient();
- PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
+ updateCurrentView();
+ }
+ else
+ {
+ if (e.getStateChange() == ItemEvent.SELECTED)
{
- searchSummaries.addAll(resultList.getSearchSummary());
-
+ updateCurrentView();
}
}
- for (PDBResponseSummary summary : searchSummaries)
- {
- jListFoundStructures.setSelectedValue(summary, true);
- // jListFoundStructures.
- break;
- }
- System.out.println("Found item count : " + searchSummaries.size());
+ }
+
+ @Override
+ public void ok_ActionPerformed()
+ {
+ // TODO code to load selected structures to jmol or chimera
}
public void pdbFromFile_actionPerformed()
}
-
// rpdbview.addActionListener(new ActionListener()
// {
//
}
}
- // public static void main(String[] args)
- // {
- // SwingUtilities.invokeLater(new Runnable()
- // {
- // public void run()
- // {
- // new StructureChooser(null, null);
- // }
- // });
- // }
-
-
}
import java.awt.CardLayout;
import java.awt.Dimension;
import java.awt.FlowLayout;
+import java.awt.Image;
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.JTable;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
protected AlignmentPanel ap;
- protected JLabel resultLabel = new JLabel("View : ");
+ protected JLabel resultLabel = new JLabel("Select : ");
protected JButton ok = new JButton();
protected JCheckBox rememberSettings = new JCheckBox("Don't ask me again");
+ protected JCheckBox invertFilter = new JCheckBox("Invert");
+
+ protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
+ "/images/loading.gif"));
+
+ protected JLabel loadingImageLabel = new JLabel(loadingImage);
protected static final String VIEWS_FILTER = "VIEWS_FILTER";
protected JList<PDBResponseSummary> jListFoundStructures = new JList<PDBResponseSummary>();
+ // protected JScrollPane foundStructuresScroller = new JScrollPane(
+ // jListFoundStructures);
+
+ protected JTable summaryTable = new JTable();
protected JScrollPane foundStructuresScroller = new JScrollPane(
- jListFoundStructures);
+ summaryTable);
public GStructureChooser()
{
try
{
jbInit();
+ mainFrame.setVisible(false);
mainFrame.invalidate();
mainFrame.pack();
} catch (Exception e)
private void jbInit() throws Exception
{
-
ok.setFont(new java.awt.Font("Verdana", 0, 12));
- ok.setText(MessageManager.getString("action.ok"));
+ ok.setText(MessageManager.getString("action.view"));
ok.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
foundStructuresScroller
.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ filterOptionsComboBox.setFont(new java.awt.Font("Verdana", 0, 12));
+ invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
+ rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
+
+ filterOptionsComboBox.addItemListener(this);
+ invertFilter.addItemListener(this);
+
actionPanel.add(rememberSettings);
actionPanel.add(ok);
actionPanel.add(cancel);
- filterOptionsComboBox.addItemListener(this);
filterPanel.add(resultLabel);
filterPanel.add(filterOptionsComboBox);
+ loadingImageLabel.setVisible(false);
+
+ filterPanel.add(loadingImageLabel);
+
+ filterPanel.add(invertFilter);
idInputPanel.setLayout(new FlowLayout());
idInputPanel.add(search);
Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
}
+
+ private ImageIcon scaleImageIcone(ImageIcon imageIcon, int width, int height)
+ {
+ Image image = imageIcon.getImage(); // transform it
+
+ Image newimg = image.getScaledInstance(width, height,
+ java.awt.Image.SCALE_SMOOTH); // scale it the smooth way
+
+ return new ImageIcon(newimg);
+ }
+
@Override
public void itemStateChanged(ItemEvent e)
{
- stateChanged();
+ stateChanged(e);
}
public class FilterOptions
this.view = view;
}
+ // public FilterOptions(PDBDocField field, String view)
+ // {
+ // this.name = "Best " + field.getName();
+ // this.value = field.getCode();
+ // this.view = view;
+ // }
+
public String getName()
{
return name;
}
}
- protected abstract void stateChanged();
+ protected abstract void stateChanged(ItemEvent e);
protected abstract void updateCurrentView();
import java.util.Objects;
import javax.swing.DefaultListModel;
+import javax.swing.table.DefaultTableModel;
import org.json.simple.JSONObject;
return defaultListModel;
}
+ public static DefaultTableModel getTableModel(PDBSearchRequest request,
+ Collection<PDBResponseSummary> summariesList)
+ {
+ DefaultTableModel model = new DefaultTableModel();
+
+ if (request.getAssociatedSequence() != null)
+ {
+ model.addColumn("Sequence");
+ }
+ for (PDBDocField field : request.getWantedFields())
+ {
+ model.addColumn(field.getName());
+ }
+
+ for (PDBResponseSummary res : summariesList)
+ {
+ model.addRow(res.getSummaryColums());
+ }
+ return model;
+ }
+
+
+
public class PDBResponseSummary
{
private String pdbId;
- private String summary;
+ private String summaryRow;
+
+ private String[] summaryColums;
+
+ private String associatedSequence;
private int width = 480;
- public PDBResponseSummary(JSONObject doc, List<PDBDocField> diplayFields)
+ public PDBResponseSummary(JSONObject doc,
+ List<PDBDocField> diplayFields, String associatedSeq)
{
StringBuilder summaryBuilder = new StringBuilder();
+ int colCounter = 0;
+ summaryColums = new String[(associatedSeq != null) ? diplayFields
+ .size() + 1 : diplayFields.size()];
+ if (associatedSeq != null)
+ {
+ this.associatedSequence = (associatedSeq.length() > 18) ? associatedSeq
+ .substring(0, 18) : associatedSeq;
+ summaryColums[0] = associatedSequence;
+ colCounter = 1;
+ }
+
for (PDBDocField field : diplayFields)
{
if (field.equals(PDBDocField.MOLECULE_TYPE)
+ getClass().getResource("/images/sugar.png")
.toString() + "\">");
}
+ summaryColums[colCounter++] = moleculeType;
}
else if (field.equals(PDBDocField.PDB_ID)
&& doc.get(PDBDocField.PDB_ID.getCode()) != null)
{
this.pdbId = doc.get(PDBDocField.PDB_ID.getCode()).toString();
+ summaryBuilder.append(this.pdbId).append(" | ");
+ summaryColums[colCounter++] = this.pdbId;
}
else if (doc.get(field.getCode()) != null)
{
summaryBuilder.append(field.getName()).append(": ")
.append(doc.get(field.getCode())).append(" | ");
+ summaryColums[colCounter++] = doc.get(field.getCode()).toString();
}
}
int endIndex = summaryBuilder.lastIndexOf(" | ");
String fSummary = summaryBuilder.toString().substring(0, endIndex);
- this.summary = fSummary.trim();
+ this.summaryRow = fSummary.trim();
summaryBuilder = null;
}
this.pdbId = pdbId;
}
- public String getSummary()
+ public String getSummaryRow()
+ {
+ return summaryRow;
+ }
+
+ public void setSummaryRow(String summary)
{
- return summary;
+ this.summaryRow = summary;
}
- public void setSummary(String summary)
+ public String[] getSummaryColums()
{
- this.summary = summary;
+ return summaryColums;
+ }
+
+ public void setSummaryColums(String[] summaryColums)
+ {
+ this.summaryColums = summaryColums;
}
public String toString()
StringBuilder html = new StringBuilder();
html.append("<html><div style=\"width:" + width
+ "; word-wrap: break-word; border-bottom-style: dotted;\"> ");
- html.append(summary);
+ html.append(summaryRow);
html.append("</div></html>");
return html.toString();
}
@Override
public int hashCode()
{
- return Objects.hash(this.pdbId, this.summary);
+ return Objects.hash(this.pdbId, this.summaryRow);
+ }
+
+ @Override
+ public boolean equals(Object other)
+ {
+ if (!(other instanceof PDBResponseSummary))
+ {
+ return false;
+ }
+
+ PDBResponseSummary that = (PDBResponseSummary) other;
+
+ // Custom equality check here.
+ return this.pdbId.equals(that.pdbId)
+ && this.summaryRow.equals(that.summaryRow);
}
+
}
}
git://source.jalview.org / jalview.git / commitdiff
