/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.List;
+import java.util.Objects;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBox;
-import javax.swing.JOptionPane;
-import javax.swing.ListSelectionModel;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
+import javax.swing.table.AbstractTableModel;
/**
* Provides the behaviors for the Structure chooser Panel
*/
@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
+ implements IProgressIndicator
{
- private boolean structuresDiscovered = false;
+ private static int MAX_QLENGTH = 7820;
private SequenceI selectedSequence;
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+ private Collection<FTSData> discoveredStructuresSet;
- private PDBRestRequest pdbRequest;
+ private FTSRestRequest lastPdbRequest;
- private PDBRestClient pdbRestCleint;
+ private FTSRestClientI pdbRestCleint;
+ private String selectedPdbFileName;
+
+ private boolean isValidPBDEntry;
+
+ private boolean cachedPDBExists;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
*/
public void init()
{
+ if (!Jalview.isHeadlessMode())
+ {
+ progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ }
+
+ chk_superpose.setSelected(Cache.getDefault("AUTOSUPERIMPOSE", true));
+
+ // ensure a filter option is in force for search
+ populateFilterComboBox(true, cachedPDBExists);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
public void run()
{
long startTime = System.currentTimeMillis();
- String msg = MessageManager.getString("status.fetching_db_refs");
- updateProgressIndicator(msg, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.loading_cached_pdb_entries"), startTime);
+ loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(MessageManager.getString(
+ "status.searching_for_pdb_structures"), startTime);
fetchStructuresMetaData();
- populateFilterComboBox();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+ discoverStructureViews();
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
discoverPDBStructuresThread.start();
}
+ private void discoverStructureViews()
+ {
+ if (Desktop.instance != null)
+ {
+ targetView.removeAllItems();
+ targetView.addItem(
+ new StructureViewer(ap.getStructureSelectionManager()));
+ if (lastTargetedView != null && !lastTargetedView.isVisible())
+ {
+ lastTargetedView = null;
+ }
+ int linkedViewsAt = 1;
+ for (StructureViewerBase view : Desktop.instance
+ .getStructureViewers(null, null))
+ {
+ StructureViewer viewHandler = (lastTargetedView != null
+ && lastTargetedView.sview == view) ? lastTargetedView
+ : StructureViewer.reconfigure(view);
+
+ if (view.isLinkedWith(ap))
+ {
+ targetView.insertItemAt(viewHandler,
+ linkedViewsAt++);
+ }
+ else
+ {
+ targetView.addItem(viewHandler);
+ }
+ }
+ targetView.setVisible(targetView.getItemCount() > 1);
+
+ // finally, restore last targeted view by default.
+ if (lastTargetedView != null)
+ {
+ targetView.setSelectedItem(lastTargetedView);
+ }
+ }
+ }
+
+ private static StructureViewer lastTargetedView = null;
+
/**
* Updates the progress indicator with the specified message
*
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);
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
+
+ discoveredStructuresSet = new LinkedHashSet<>();
+ HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(");
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
+ !chk_invertFilter.isSelected());
+ pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ pdbRequest.setAssociatedSequence(seq);
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ errors.add(e.getMessage());
+ continue;
+ }
+ lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
- updateSequenceDbRef(seq, resultList.getSearchSummary());
}
}
int noOfStructuresFound = 0;
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- jList_FoundStructures.setModel(PDBRestResponse
- .getListModel(discoveredStructuresSet));
- tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
- discoveredStructuresSet));
- // resizeColumnWidth(summaryTable);
- structuresDiscovered = true;
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_no_of_structures",
+ noOfStructuresFound, totalTime));
+ }
+ else
+ {
+ mainFrame.setTitle(MessageManager
+ .getString("label.structure_chooser_manual_association"));
+ if (errors.size() > 0)
+ {
+ StringBuilder errorMsg = new StringBuilder();
+ for (String error : errors)
+ {
+ errorMsg.append(error).append("\n");
+ }
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
+ MessageManager.getString("label.pdb_web-service_error"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
}
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
- + " Found (" + totalTime + ")");
}
- /**
- * Update the DBRef entry for a given sequence with values retrieved from
- * PDBResponseSummary
- *
- * @param seq
- * the Sequence to update its DBRef entry
- * @param responseSummaries
- * a collection of PDBResponseSummary
- */
- public void updateSequenceDbRef(SequenceI seq,
- Collection<PDBResponseSummary> responseSummaries)
+ public void loadLocalCachedPDBEntries()
{
- for (PDBResponseSummary response : responseSummaries)
+ ArrayList<CachedPDB> entries = new ArrayList<>();
+ for (SequenceI seq : selectedSequences)
{
- PDBEntry newEntry = new PDBEntry();
- newEntry.setId(response.getPdbId());
- newEntry.setType("PDB");
- seq.getDatasetSequence().addPDBId(newEntry);
+ if (seq.getDatasetSequence() != null
+ && seq.getDatasetSequence().getAllPDBEntries() != null)
+ {
+ for (PDBEntry pdbEntry : seq.getDatasetSequence()
+ .getAllPDBEntries())
+ {
+ if (pdbEntry.getFile() != null)
+ {
+ entries.add(new CachedPDB(seq, pdbEntry));
+ }
+ }
+ }
}
+ cachedPDBExists = !entries.isEmpty();
+ PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
+ tbl_local_pdb.setModel(tableModelx);
}
/**
* the sequences to build a query for
* @return the built query string
*/
- @SuppressWarnings("unchecked")
+
public static String buildQuery(SequenceI seq)
{
- String query = seq.getName();
+ boolean isPDBRefsFound = false;
+ boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- int count = 0;
+ Set<String> seqRefs = new LinkedHashSet<>();
+
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
+ {
+ for (PDBEntry entry : seq.getAllPDBEntries())
+ {
+ if (isValidSeqName(entry.getId()))
+ {
+ queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
+ .append(" OR ");
+ isPDBRefsFound = true;
+ }
+ }
+ }
- if (seq.getPDBId() != null)
+ if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
{
- for (PDBEntry entry : (Vector<PDBEntry>) seq.getPDBId())
+ for (DBRefEntry dbRef : seq.getDBRefs())
{
- queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGTH)
+ {
+ if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+ {
+ queryBuilder.append("uniprot_accession:")
+ .append(getDBRefId(dbRef)).append(" OR ");
+ queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+ .append(" OR ");
+ isUniProtRefsFound = true;
+ }
+ else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
+ {
+
+ queryBuilder.append("pdb_id:")
+ .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
+ isPDBRefsFound = true;
+ }
+ else
+ {
+ seqRefs.add(getDBRefId(dbRef));
+ }
+ }
}
}
- if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+ if (!isPDBRefsFound && !isUniProtRefsFound)
{
- for (DBRefEntry dbRef : seq.getDBRef())
+ String seqName = seq.getName();
+ seqName = sanitizeSeqName(seqName);
+ String[] names = seqName.toLowerCase().split("\\|");
+ for (String name : names)
{
- queryBuilder.append("text:")
- .append(dbRef.getAccessionId().replaceAll("GO:", ""))
- .append(" OR ");
- ++count;
- if (count > 10)
+ // System.out.println("Found name : " + name);
+ name.trim();
+ if (isValidSeqName(name))
{
- break;
+ seqRefs.add(name);
}
}
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- query = queryBuilder.toString().substring(5, endIndex);
+
+ for (String seqRef : seqRefs)
+ {
+ queryBuilder.append("text:").append(seqRef).append(" OR ");
+ }
+ }
+
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ if (queryBuilder.toString().length() < 6)
+ {
+ return null;
}
- // System.out.println("Query -----> " + query);
+ String query = queryBuilder.toString().substring(0, endIndex);
return query;
}
/**
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ static String sanitizeSeqName(String seqName)
+ {
+ Objects.requireNonNull(seqName);
+ return seqName.replaceAll("\\[\\d*\\]", "")
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
+ }
+
+ /**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ public static boolean isValidSeqName(String seqName)
+ {
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase();
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ /**
* Filters a given list of discovered structures based on supplied argument
*
* @param fieldToFilterBy
@Override
public void run()
{
- try
- {
- lbl_loading.setVisible(true);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
+ long startTime = System.currentTimeMillis();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ lbl_loading.setVisible(true);
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
+ Collection<FTSData> filteredResponse = new HashSet<>();
+ HashSet<String> errors = new HashSet<>();
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
- for (SequenceI seq : selectedSequences)
+ for (SequenceI seq : selectedSequences)
+ {
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
{
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint
- .executeRequest(pdbRequest);
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- filteredResponse.addAll(resultList.getSearchSummary());
- }
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ pdbRequest.setFacet(true);
+ pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
+ pdbRequest.setFacetPivotMinCount(1);
}
+ else
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ }
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ errors.add(e.getMessage());
+ continue;
+ }
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
- if (filteredResponse != null)
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, reorderedStructuresSet));
+
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields, tempUserPrefs);
+ getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
+ getResultTable().getColumn("Ref Sequence").setMinWidth(100);
+ getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
+ // Update table selection model here
+ getResultTable().addRowSelectionInterval(0,
+ filterResponseCount - 1);
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_filter_time", totalTime));
+ }
+ else
+ {
+ mainFrame.setTitle(MessageManager.formatMessage(
+ "label.structure_chooser_filter_time", totalTime));
+ if (errors.size() > 0)
{
- int filterResponseCount = filteredResponse.size();
- List<PDBResponseSummary> originalDiscoveredStructuresList = new ArrayList<PDBResponseSummary>(
- discoveredStructuresSet);
- originalDiscoveredStructuresList.removeAll(filteredResponse);
-
- Collection<PDBResponseSummary> reorderedStructuresSet = new ArrayList<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++)
+ StringBuilder errorMsg = new StringBuilder();
+ for (String error : errors)
{
- // filterIndice[x] = x;
- model.addSelectionInterval(x, x);
+ errorMsg.append(error).append("\n");
}
-
- // Discard unwanted objects to make them eligible for garbage
- // collection
- originalDiscoveredStructuresList = null;
- reorderedStructuresSet = null;
-
- // jListFoundStructures.setSelectedIndices(filterIndice);
+ JvOptionPane.showMessageDialog(null, errorMsg.toString(),
+ MessageManager.getString("label.pdb_web-service_error"),
+ JvOptionPane.ERROR_MESSAGE);
}
-
- lbl_loading.setVisible(false);
- } catch (Exception e)
- {
- e.printStackTrace();
}
+
+ lbl_loading.setVisible(false);
+
+ validateSelections();
}
});
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
*/
+ @Override
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.setDialogTitle(
+ MessageManager.formatMessage("label.select_pdb_file_for",
+ selectedSequence.getDisplayId(false)));
chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new String[]
- { selectedSequence.getDisplayId(false) }));
+ "label.load_pdb_file_associate_with_sequence",
+ selectedSequence.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, selectedSequence, true,
- Desktop.instance);
+ selectedPdbFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ validateSelections();
}
}
/**
- * Handles action event for btn_ok
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
*/
- @Override
- public void ok_ActionPerformed()
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExist)
{
- int pdbIdCol = getPDBIdColumIndex(pdbRequest.getWantedFields());
- int[] selectedRows = tbl_summary.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- for (int summaryRow : selectedRows)
+ /*
+ * temporarily suspend the change listener behaviour
+ */
+ cmb_filterOption.removeItemListener(this);
+
+ cmb_filterOption.removeAllItems();
+ if (haveData)
+ {
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_quality"),
+ "overall_quality", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_resolution"),
+ "resolution", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_protein_chain"),
+ "number_of_protein_chains", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_bound_molecules"),
+ "number_of_bound_molecules", VIEWS_FILTER, false));
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_polymer_residues"),
+ "number_of_polymer_residues", VIEWS_FILTER, true));
+ }
+ cmb_filterOption.addItem(
+ new FilterOption(MessageManager.getString("label.enter_pdb_id"),
+ "-", VIEWS_ENTER_ID, false));
+ cmb_filterOption.addItem(
+ new FilterOption(MessageManager.getString("label.from_file"),
+ "-", VIEWS_FROM_FILE, false));
+
+ if (cachedPDBExist)
{
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
- .toString();
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType("PDB");
- pdbEntriesToView[count++] = pdbEntry;
+ FilterOption cachedOption = new FilterOption(
+ MessageManager.getString("label.cached_structures"),
+ "-", VIEWS_LOCAL_PDB, false);
+ cmb_filterOption.addItem(cachedOption);
+ cmb_filterOption.setSelectedItem(cachedOption);
}
- new StructureViewer(ap.getStructureSelectionManager()).viewStructures(
- ap, pdbEntriesToView, ap.av.collateForPDB(pdbEntriesToView));
+
+ cmb_filterOption.addItemListener(this);
}
/**
- * Handles action event for manual entry of pdb ids
+ * Updates the displayed view based on the selected filter option
*/
- public void enterPDB_actionPerformed()
+ protected void updateCurrentView()
{
- 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)
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ layout_switchableViews.show(pnl_switchableViews,
+ selectedFilterOpt.getView());
+ String filterTitle = mainFrame.getTitle();
+ mainFrame.setTitle(frameTitle);
+ chk_invertFilter.setVisible(false);
+ if (selectedFilterOpt.getView() == VIEWS_FILTER)
{
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- selectedSequence.getDatasetSequence().addPDBId(entry);
+ mainFrame.setTitle(filterTitle);
+ chk_invertFilter.setVisible(true);
+ filterResultSet(selectedFilterOpt.getValue());
}
+ else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
+ || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
+ {
+ mainFrame.setTitle(MessageManager
+ .getString("label.structure_chooser_manual_association"));
+ idInputAssSeqPanel.loadCmbAssSeq();
+ fileChooserAssSeqPanel.loadCmbAssSeq();
+ }
+ validateSelections();
}
/**
- * Populates the filter combo-box options dynamically depending on discovered
- * structures
+ * Validates user selection and activates the view button if all parameters
+ * are correct
*/
- protected void populateFilterComboBox()
+ @Override
+ public void validateSelections()
{
- if (isStructuresDiscovered())
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ btn_view.setEnabled(false);
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
{
- cmb_filterOption.addItem(new FilterOption("Best Quality",
- PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
- PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Resolution",
- PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
- PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
- PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
- PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+ if (getResultTable().getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ if (tbl_local_pdb.getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ validateAssociationEnterPdb();
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ validateAssociationFromFile();
}
- cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
- cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE));
}
/**
- * Updates the displayed view based on the selected filter option
+ * Validates inputs from the Manual PDB entry panel
*/
- protected void updateCurrentView()
+ public void validateAssociationEnterPdb()
{
- FilterOption selectedOption = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- layout_switchableViews.show(pnl_switchableViews,
- selectedOption.getView());
- chk_invertFilter.setEnabled(false);
- if (selectedOption.getView() == VIEWS_FILTER)
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ if (txt_search.getText().length() > 0)
+ {
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage("info.no_pdb_entry_found_for",
+ txt_search.getText())));
+ }
+
+ if (errorWarning.length() > 0)
+ {
+ lbl_pdbManualFetchStatus.setIcon(warningImage);
+ lbl_pdbManualFetchStatus.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
+ }
+
+ if (selectedSequences.length == 1 || !assSeqOpt.getName()
+ .equalsIgnoreCase("-Select Associated Seq-"))
+ {
+ txt_search.setEnabled(true);
+ if (isValidPBDEntry)
+ {
+ btn_view.setEnabled(true);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ 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
{
- chk_invertFilter.setEnabled(true);
- filterResultSet(selectedOption.getValue());
+ btn_pdbFromFile.setEnabled(false);
+ lbl_fromFileStatus.setIcon(errorImage);
}
}
+ @Override
+ public void cmbAssSeqStateChanged()
+ {
+ validateSelections();
+ }
+
/**
* Handles the state change event for the 'filter' combo-box and 'invert'
* check-box
}
+ /**
+ * select structures for viewing by their PDB IDs
+ *
+ * @param pdbids
+ * @return true if structures were found and marked as selected
+ */
+ public boolean selectStructure(String... pdbids)
+ {
+ boolean found = false;
+
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+ : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
- public boolean isStructuresDiscovered()
+ if (restable == null)
+ {
+ // can't select (enter PDB ID, or load file - need to also select which
+ // sequence to associate with)
+ return false;
+ }
+
+ int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
+ for (int r = 0; r < restable.getRowCount(); r++)
+ {
+ for (int p = 0; p < pdbids.length; p++)
+ {
+ if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
+ .equalsIgnoreCase(pdbids[p]))
+ {
+ restable.setRowSelectionInterval(r, r);
+ found = true;
+ }
+ }
+ }
+ return found;
+ }
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
+ {
+ showStructures(false);
+ }
+
+ /**
+ * structure viewer opened by this dialog, or null
+ */
+ private StructureViewer sViewer = null;
+
+ public void showStructures(boolean waitUntilFinished)
+ {
+
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+
+ final int preferredHeight = pnl_filter.getHeight();
+
+ Runnable viewStruc = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+ : tbl_local_pdb;
+
+ if (currentView == VIEWS_FILTER)
+ {
+ int pdbIdColIndex = restable.getColumn("PDB Id")
+ .getModelIndex();
+ int refSeqColIndex = restable.getColumn("Ref Sequence")
+ .getModelIndex();
+ int[] selectedRows = restable.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
+ for (int row : selectedRows)
+ {
+ String pdbIdStr = restable
+ .getValueAt(row, pdbIdColIndex).toString();
+ SequenceI selectedSeq = (SequenceI) restable
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = getFindEntry(pdbIdStr,
+ selectedSeq.getAllPDBEntries());
+ }
+
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
+ .getModelIndex();
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ if (pdbIdStr.split(":").length > 1)
+ {
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
+ }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
+
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ new SequenceI[]
+ { selectedSequence });
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
+
+ sViewer = launchStructureViewer(
+ ssm, new PDBEntry[]
+ { fileEntry }, ap,
+ new SequenceI[]
+ { selectedSequence });
+ }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ closeAction(preferredHeight);
+ mainFrame.dispose();
+ }
+ });
+ }
+ };
+ Thread runner = new Thread(viewStruc);
+ runner.start();
+ if (waitUntilFinished)
+ {
+ while (sViewer == null ? runner.isAlive()
+ : (sViewer.sview == null ? true
+ : !sViewer.sview.hasMapping()))
+ {
+ try
+ {
+ Thread.sleep(300);
+ } catch (InterruptedException ie)
+ {
+
+ }
+ }
+ }
+ }
+
+ private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ {
+ Objects.requireNonNull(id);
+ Objects.requireNonNull(pdbEntries);
+ PDBEntry foundEntry = null;
+ for (PDBEntry entry : pdbEntries)
+ {
+ if (entry.getId().equalsIgnoreCase(id))
+ {
+ return entry;
+ }
+ }
+ return foundEntry;
+ }
+
+ /**
+ * @param ssm
+ * @return targetted structure view (new or existing) configured according to
+ * superpose checkbox
+ */
+ public StructureViewer getTargetedStructureViewer(
+ StructureSelectionManager ssm)
+ {
+ Object _sv = targetView.getSelectedItem();
+ StructureViewer sv;
+ if (_sv == null)
+ {
+ sv = new StructureViewer(ssm);
+ } else {
+ sv = (StructureViewer) _sv;
+ }
+ sv.setSuperpose(chk_superpose.isSelected());
+ return sv;
+ }
+ private StructureViewer launchStructureViewer(
+ StructureSelectionManager ssm,
+ final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences)
+ {
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
+ final StructureViewer sViewer = getTargetedStructureViewer(ssm);
+ sViewer.setSuperpose(chk_superpose.isSelected());
+
+ setProgressBar(null, progressId);
+ if (SiftsSettings.isMapWithSifts())
+ {
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
+ int p = 0;
+ // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+ // real PDB ID. For moment, we can also safely do this if there is already
+ // a known mapping between the PDBEntry and the sequence.
+ for (SequenceI seq : sequences)
+ {
+ PDBEntry pdbe = pdbEntriesToView[p++];
+ if (pdbe != null && pdbe.getFile() != null)
+ {
+ StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+ if (smm != null && smm.length > 0)
+ {
+ for (StructureMapping sm : smm)
+ {
+ if (sm.getSequence() == seq)
+ {
+ continue;
+ }
+ }
+ }
+ }
+ if (seq.getPrimaryDBRefs().size() == 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ }
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y), progressId);
+ SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
+ int x = 0;
+ for (SequenceI fSeq : seqsWithoutSourceDBRef)
+ {
+ seqWithoutSrcDBRef[x++] = fSeq;
+ }
+
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
+
+ setProgressBar("Fetch complete.", progressId); // todo i18n
+ }
+ }
+ if (pdbEntriesToView.length > 1)
+ {
+ setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ }
+ else
+ {
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()),progressId);
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ }
+ setProgressBar(null, progressId);
+ // remember the last viewer we used...
+ lastTargetedView = sViewer;
+ return sViewer;
+ }
+
+ /**
+ * Populates the combo-box used in associating manually fetched structures to
+ * a unique sequence when more than one sequence selection is made.
+ */
+ @Override
+ public void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq,
+ JLabel lbl_associateSeq)
{
- return structuresDiscovered;
+ cmb_assSeq.removeAllItems();
+ cmb_assSeq.addItem(
+ new AssociateSeqOptions("-Select Associated Seq-", 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 void setStructuresDiscovered(boolean structuresDiscovered)
+ public boolean isStructuresDiscovered()
{
- this.structuresDiscovered = structuresDiscovered;
+ return discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty();
}
- public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ public Collection<FTSData> getDiscoveredStructuresSet()
{
return discoveredStructuresSet;
}
+
+ @Override
+ protected void txt_search_ActionPerformed()
+ {
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
+ {
+ String searchTerm = txt_search.getText().toLowerCase();
+ searchTerm = searchTerm.split(":")[0];
+ // System.out.println(">>>>> search term : " + searchTerm);
+ List<FTSDataColumnI> wantedFields = new ArrayList<>();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(searchTerm + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence);
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
+ }
+ validateSelections();
+ }
+ }.start();
+ }
+
+ @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();
+ }
+ }
+
+ public class PDBEntryTableModel extends AbstractTableModel
+ {
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
+ "File" };
+
+ private List<CachedPDB> pdbEntries;
+
+ public PDBEntryTableModel(List<CachedPDB> pdbEntries)
+ {
+ this.pdbEntries = new ArrayList<>(pdbEntries);
+ }
+
+ @Override
+ public String getColumnName(int columnIndex)
+ {
+ return columns[columnIndex];
+ }
+
+ @Override
+ public int getRowCount()
+ {
+ return pdbEntries.size();
+ }
+
+ @Override
+ public int getColumnCount()
+ {
+ return columns.length;
+ }
+
+ @Override
+ public boolean isCellEditable(int row, int column)
+ {
+ return false;
+ }
+
+ @Override
+ public Object getValueAt(int rowIndex, int columnIndex)
+ {
+ Object value = "??";
+ CachedPDB entry = pdbEntries.get(rowIndex);
+ switch (columnIndex)
+ {
+ case 0:
+ value = entry.getSequence();
+ break;
+ case 1:
+ value = entry.getPdbEntry();
+ break;
+ case 2:
+ value = entry.getPdbEntry().getChainCode() == null ? "_"
+ : entry.getPdbEntry().getChainCode();
+ break;
+ case 3:
+ value = entry.getPdbEntry().getType();
+ break;
+ case 4:
+ value = entry.getPdbEntry().getFile();
+ break;
+ }
+ return value;
+ }
+
+ @Override
+ public Class<?> getColumnClass(int columnIndex)
+ {
+ return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
+ }
+
+ public CachedPDB getPDBEntryAt(int row)
+ {
+ return pdbEntries.get(row);
+ }
+
+ }
+
+ private class CachedPDB
+ {
+ private SequenceI sequence;
+
+ private PDBEntry pdbEntry;
+
+ public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
+ {
+ this.sequence = sequence;
+ this.pdbEntry = pdbEntry;
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public PDBEntry getPdbEntry()
+ {
+ return pdbEntry;
+ }
+
+ }
+
+ private IProgressIndicator progressBar;
+
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ progressBar.setProgressBar(message, id);
+ }
+
+ @Override
+ public void registerHandler(long id, IProgressIndicatorHandler handler)
+ {
+ progressBar.registerHandler(id, handler);
+ }
+
+ @Override
+ public boolean operationInProgress()
+ {
+ return progressBar.operationInProgress();
+ }
+
+ public JalviewStructureDisplayI getOpenedStructureViewer()
+ {
+ return sViewer == null ? null : sViewer.sview;
+ }
}
git://source.jalview.org / jalview.git / blobdiff