/*
+
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
import jalview.util.MessageManager;
import jalview.ws.dbsources.PDBRestClient;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBox;
-import javax.swing.JOptionPane;
-import javax.swing.ListSelectionModel;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
/**
* Provides the behaviors for the Structure chooser Panel
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+ private Collection<PDBResponseSummary> discoveredStructuresSet;
- private PDBRestRequest pdbRequest;
+ private PDBRestRequest lastPdbRequest;
private PDBRestClient pdbRestCleint;
+ private String selectedPdbFileName;
+
+ private boolean isValidPBDEntry;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- 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);
- pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setWantedFields(wantedFields);
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+
+ discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
for (SequenceI seq : selectedSequences)
{
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- jList_FoundStructures.setModel(PDBRestResponse
- .getListModel(discoveredStructuresSet));
- tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
+ tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
- // resizeColumnWidth(summaryTable);
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
}
int endIndex = queryBuilder.lastIndexOf(" OR ");
query = queryBuilder.toString().substring(5, endIndex);
}
- // System.out.println("Query -----> " + query);
return query;
}
*/
public void filterResultSet(final String fieldToFilterBy)
{
+
+ // SwingWorker aWorker = new SwingWorker()
+ // {
+ // long startTime = System.currentTimeMillis();
+ //
+ // @Override
+ // protected Object doInBackground() throws Exception
+ // {
+ // lbl_loading.setVisible(true);
+ //
+ // Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ // .getStructureSummaryFields();
+ // Collection<PDBResponseSummary> filteredResponse = new
+ // HashSet<PDBResponseSummary>();
+ // for (SequenceI seq : selectedSequences)
+ // {
+ // PDBRestRequest pdbRequest = new PDBRestRequest();
+ // pdbRequest.setAllowEmptySeq(false);
+ // pdbRequest.setResponseSize(1);
+ // pdbRequest.setFieldToSearchBy("(text:");
+ // pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ // !chk_invertFilter.isSelected());
+ // pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ // pdbRequest.setWantedFields(wantedFields);
+ // pdbRequest.setAssociatedSequence(seq.getName());
+ // pdbRestCleint = new PDBRestClient();
+ // PDBRestResponse resultList = pdbRestCleint
+ // .executeRequest(pdbRequest);
+ // lastPdbRequest = pdbRequest;
+ // if (resultList.getSearchSummary() != null
+ // && !resultList.getSearchSummary().isEmpty())
+ // {
+ // filteredResponse.addAll(resultList.getSearchSummary());
+ // }
+ // }
+ //
+ // if (!filteredResponse.isEmpty())
+ // {
+ // final int filterResponseCount = filteredResponse.size();
+ // Collection<PDBResponseSummary> reorderedStructuresSet = new
+ // LinkedHashSet<PDBResponseSummary>();
+ // reorderedStructuresSet.addAll(filteredResponse);
+ // reorderedStructuresSet.addAll(discoveredStructuresSet);
+ // tbl_summary.setModel(PDBRestResponse.getTableModel(
+ // lastPdbRequest, reorderedStructuresSet));
+ //
+ // // Update the model here
+ // // ListSelectionModel model = tbl_summary.getSelectionModel();
+ // // model.clearSelection();
+ // // model.addSelectionInterval(0, filterResponseCount - 1);
+ // // EventQueue.invokeLater(new Runnable()
+ // // {
+ // // public void run()
+ // // {
+ // // tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+ //
+ // // }
+ // // });
+ // // Discard unwanted objects to make them eligible for garbage
+ // // collection
+ // reorderedStructuresSet = null;
+ // }
+ // return null;
+ // }
+ //
+ // public void done()
+ // {
+ // lbl_loading.setVisible(false);
+ // tbl_summary.addRowSelectionInterval(0, 2);
+ // String totalTime = (System.currentTimeMillis() - startTime)
+ // + " milli secs";
+ // mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime
+ // + ")");
+ // validateSelections();
+ // }
+ // };
+ // aWorker.execute();
+
Thread filterThread = new Thread(new Runnable()
{
@Override
public void run()
{
+ long startTime = System.currentTimeMillis();
try
{
lbl_loading.setVisible(true);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
for (SequenceI seq : selectedSequences)
{
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList = pdbRestCleint
.executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
}
}
- if (filteredResponse != null)
+ if (!filteredResponse.isEmpty())
{
- int filterResponseCount = filteredResponse.size();
- List<PDBResponseSummary> originalDiscoveredStructuresList = new ArrayList<PDBResponseSummary>(
- discoveredStructuresSet);
- originalDiscoveredStructuresList.removeAll(filteredResponse);
-
- Collection<PDBResponseSummary> reorderedStructuresSet = new ArrayList<PDBResponseSummary>();
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
reorderedStructuresSet.addAll(filteredResponse);
- reorderedStructuresSet.addAll(originalDiscoveredStructuresList);
-
- jList_FoundStructures.setModel(PDBRestResponse
- .getListModel(reorderedStructuresSet));
- tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
- reorderedStructuresSet));
-
- // int[] filterIndice = new int[filterResponseCount];
- ListSelectionModel model = tbl_summary.getSelectionModel();
- model.clearSelection();
- for (int x = 0; x < filterResponseCount; x++)
- {
- // filterIndice[x] = x;
- model.addSelectionInterval(x, x);
- }
-
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ tbl_summary.setModel(PDBRestResponse.getTableModel(
+ lastPdbRequest, reorderedStructuresSet));
+
+ // Update the model here
+ // ListSelectionModel model = tbl_summary.getSelectionModel();
+ // model.clearSelection();
+ // model.addSelectionInterval(0, filterResponseCount - 1);
+ // EventQueue.invokeLater(new Runnable()
+ // {
+ // public void run()
+ // {
+ tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+
+ // }
+ // });
// Discard unwanted objects to make them eligible for garbage
// collection
- originalDiscoveredStructuresList = null;
reorderedStructuresSet = null;
-
- // jListFoundStructures.setSelectedIndices(filterIndice);
}
lbl_loading.setVisible(false);
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+
+ validateSelections();
} catch (Exception e)
{
e.printStackTrace();
filterThread.start();
}
- /**
- * Determines the column index for the pdb id in the summary table. The pdb id
- * serves as a unique identifier for a given row in the summary table
- *
- * @param wantedFeilds
- * the available table columns in no particular order
- * @return the pdb id field column index
- */
- public static int getPDBIdColumIndex(Collection<PDBDocField> wantedFeilds)
- {
- int pdbFeildIndex = 1;
- for (PDBDocField feild : wantedFeilds)
- {
- if (feild.equals(PDBDocField.PDB_ID))
- {
- break;
- }
- ++pdbFeildIndex;
- }
- return pdbFeildIndex;
- }
/**
* Handles action event for btn_pdbFromFile
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, selectedSequence, true,
- Desktop.instance);
- }
- }
-
- /**
- * Handles action event for btn_ok
- */
- @Override
- public void ok_ActionPerformed()
- {
- int pdbIdCol = getPDBIdColumIndex(pdbRequest.getWantedFields());
- int[] selectedRows = tbl_summary.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- for (int summaryRow : selectedRows)
- {
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
- .toString();
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType("PDB");
- pdbEntriesToView[count++] = pdbEntry;
- }
- new StructureViewer(ap.getStructureSelectionManager()).viewStructures(
- ap, pdbEntriesToView, ap.av.collateForPDB(pdbEntriesToView));
- }
-
- /**
- * Handles action event for manual entry of pdb ids
- */
- 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());
- selectedSequence.getDatasetSequence().addPDBId(entry);
+ selectedPdbFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ validateSelections();
}
}
*/
protected void updateCurrentView()
{
- FilterOption selectedOption = ((FilterOption) cmb_filterOption
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
layout_switchableViews.show(pnl_switchableViews,
- selectedOption.getView());
- chk_invertFilter.setEnabled(false);
- if (selectedOption.getView() == VIEWS_FILTER)
+ selectedFilterOpt.getView());
+ String filterTitle = mainFrame.getTitle();
+ mainFrame.setTitle(frameTitle);
+ chk_invertFilter.setVisible(false);
+ if (selectedFilterOpt.getView() == VIEWS_FILTER)
+ {
+ mainFrame.setTitle(filterTitle);
+ chk_invertFilter.setVisible(true);
+ filterResultSet(selectedFilterOpt.getValue());
+ }
+ else
{
- chk_invertFilter.setEnabled(true);
- filterResultSet(selectedOption.getValue());
+ idInputAssSeqPanel.loadCmbAssSeq();
+ fileChooserAssSeqPanel.loadCmbAssSeq();
}
+ validateSelections();
+ }
+
+ /**
+ * Validates user selection and activates the view button if all parameters
+ * are correct
+ */
+ public void validateSelections()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ btn_view.setEnabled(false);
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ if (tbl_summary.getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ validateAssociationEnterPdb();
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ validateAssociationFromFile();
+ }
+ }
+
+ /**
+ * Validates inputs from the Manual PDB entry panel
+ */
+ public void validateAssociationEnterPdb()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-"))
+ {
+ txt_search.setEnabled(true);
+ if (isValidPBDEntry)
+ {
+ btn_view.setEnabled(true);
+ lbl_pdbManualFetchStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ txt_search.setEnabled(false);
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ }
+ }
+
+ /**
+ * Validates inputs for the manual PDB file selection options
+ */
+ public void validateAssociationFromFile()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_fromFileStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null
+ && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
+ {
+ btn_pdbFromFile.setEnabled(true);
+ if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ {
+ btn_view.setEnabled(true);
+ lbl_fromFileStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ btn_pdbFromFile.setEnabled(false);
+ lbl_fromFileStatus.setIcon(errorImage);
+ }
+ }
+
+ @Override
+ public void cmbAssSeqStateChanged()
+ {
+ validateSelections();
}
/**
}
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
+ lastPdbRequest.getWantedFields(), true);
+ int[] selectedRows = tbl_summary.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int summaryRow : selectedRows)
+ {
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ .toString();
+ PDBEntry pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType("PDB");
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pdbEntriesToView,
+ ap.av.collateForPDB(pdbEntriesToView));
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ PDBEntry pdbEntry = new PDBEntry();
+ pdbEntry.setId(txt_search.getText());
+ pdbEntry.setType("PDB");
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ PDBEntry[] pdbEntriesToView = new PDBEntry[]
+ { pdbEntry };
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pdbEntriesToView,
+ ap.av.collateForPDB(pdbEntriesToView));
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+ selectedSequence, true, Desktop.instance);
+ }
+ mainFrame.dispose();
+ }
+
+ /**
+ * Populates the combo-box used in associating manually fetched structures to
+ * a unique sequence when more than one sequence selection is made.
+ */
+ public void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
+ {
+ cmb_assSeq.removeAllItems();
+ cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
+ null));
+ // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
+ lbl_associateSeq.setVisible(false);
+ if (selectedSequences.length > 1)
+ {
+ for (SequenceI seq : selectedSequences)
+ {
+ cmb_assSeq.addItem(new AssociateSeqOptions(seq));
+ }
+ }
+ else
+ {
+ String seqName = selectedSequence.getDisplayId(false);
+ seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+ lbl_associateSeq.setText(seqName);
+ lbl_associateSeq.setVisible(true);
+ cmb_assSeq.setVisible(false);
+ }
+ }
public boolean isStructuresDiscovered()
{
{
return discoveredStructuresSet;
}
+
+ @Override
+ protected void txt_search_ActionPerformed()
+ {
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(txt_search.getText() + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
+ }
+ validateSelections();
+ }
+
+ @Override
+ public void tabRefresh()
+ {
+ if (selectedSequences != null)
+ {
+ Thread refreshThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ fetchStructuresMetaData();
+ filterResultSet(((FilterOption) cmb_filterOption
+ .getSelectedItem()).getValue());
+ }
+ });
+ refreshThread.start();
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff