import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
+import jalview.jbgui.FilterOption;
import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.GStructureChooser.FilterOption;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import java.util.Objects;
import java.util.Set;
import java.util.Vector;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.Executor;
+import java.util.concurrent.Executors;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
private boolean cachedPDBExists;
+ private Collection<FTSData> lastDiscoveredStructuresSet;
+
private static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
{
// which FTS engine to use
data = StructureChooserQuerySource
- .getTDBfts();
+ .getQuerySourceFor(selectedSeqs);
initDialog();
this.ap = ap;
// ensure a filter option is in force for search
populateFilterComboBox(true, cachedPDBExists);
- Thread discoverPDBStructuresThread = new Thread(new Runnable()
+ // todo change to futures I guess
+
+ final Runnable discoverPDBStructures = new Runnable()
{
@Override
public void run()
{
+ // looks for any existing structures already loaded
+ // for the sequences (the cached ones)
+ // then queries the StructureChooserQuerySource to
+ // discover more structures.
+ //
+ // Possible optimisation is to only begin querying
+ // the structure chooser if there are no cached structures.
+
long startTime = System.currentTimeMillis();
updateProgressIndicator(MessageManager
.getString("status.loading_cached_pdb_entries"), startTime);
mainFrame.setVisible(true);
updateCurrentView();
}
- });
- discoverPDBStructuresThread.start();
+ };
+ final List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+
+ final Runnable discoverCanonicalDBrefs = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ long progressId = System.currentTimeMillis();
+
+ int y = seqsWithoutSourceDBRef.size();
+ setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y), progressId);
+ SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
+
+ setProgressBar("Fetch complete.", progressId); // todo i18n
+
+ SwingUtilities.invokeLater(discoverPDBStructures);
+ }
+ };
+
+ Executors.defaultThreadFactory().newThread(new Runnable()
+ {
+ public void run()
+ {
+
+ for (SequenceI seq : selectedSequences)
+ {
+ if (seq.isProtein())
+ {
+ int dbRef = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (dbRef < 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ }
+ }
+ // retrieve database refs for protein sequences
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ JvOptionPane.newOptionDialog(Desktop.getDesktop())
+ .setResponseHandler(0, discoverCanonicalDBrefs)
+ .setResponseHandler(1, discoverPDBStructures)
+ .showDialog(MessageManager.formatMessage("label.fetch_references_for",seqsWithoutSourceDBRef.size()), MessageManager.getString(
+ "label.fetch_uniprot_references"),
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.PLAIN_MESSAGE, null, new Object[]
+ { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") },
+ MessageManager.getString("action.ok"));
+ } else {
+ // get structures directly
+ Executors.defaultThreadFactory().newThread(discoverPDBStructures).start();
+ }
+ };
+ }).start();;
+
}
/**
{
getResultTable()
.setModel(data.getTableModel(discoveredStructuresSet));
+
noOfStructuresFound = discoveredStructuresSet.size();
+ lastDiscoveredStructuresSet=discoveredStructuresSet;
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
noOfStructuresFound, totalTime));
{
Thread filterThread = new Thread(new Runnable()
{
+
@Override
public void run()
{
FTSRestResponse resultList;
try
{
- resultList = data.selectFirstRankedQuery(seq, wantedFields,
+ resultList = data.selectFirstRankedQuery(seq, discoveredStructuresSet,wantedFields,
fieldToFilterBy, !chk_invertFilter.isSelected());
} catch (Exception e)
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable()
.setModel(data.getTableModel(reorderedStructuresSet));
-
+
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
protected void populateFilterComboBox(boolean haveData,
boolean cachedPDBExist)
{
+ populateFilterComboBox(haveData, cachedPDBExist, null);
+ }
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExist, FilterOption lastSel)
+ {
+
/*
* temporarily suspend the change listener behaviour
*/
cmb_filterOption.removeItemListener(this);
-
+ int selSet=-1;
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));
+ List<FilterOption> filters = data.getAvailableFilterOptions(VIEWS_FILTER);
+ data.updateAvailableFilterOptions(VIEWS_FILTER, filters, lastDiscoveredStructuresSet);
+ int p=0;
+ for (FilterOption filter:filters)
+ {
+ if (lastSel!=null && filter.equals(lastSel)) {
+ selSet=p;
+ }
+ p++;
+ cmb_filterOption.addItem(filter);
+ }
}
cmb_filterOption.addItem(
new FilterOption(MessageManager.getString("label.enter_pdb_id"),
- "-", VIEWS_ENTER_ID, false));
+ "-", VIEWS_ENTER_ID, false,null));
cmb_filterOption.addItem(
new FilterOption(MessageManager.getString("label.from_file"),
- "-", VIEWS_FROM_FILE, false));
+ "-", VIEWS_FROM_FILE, false,null));
if (cachedPDBExist)
{
FilterOption cachedOption = new FilterOption(
MessageManager.getString("label.cached_structures"), "-",
- VIEWS_LOCAL_PDB, false);
+ VIEWS_LOCAL_PDB, false,null);
cmb_filterOption.addItem(cachedOption);
- cmb_filterOption.setSelectedItem(cachedOption);
+ if (selSet==-1) {
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
+ }
+ if (selSet>-1)
+ {
+ cmb_filterOption.setSelectedIndex(selSet);
}
-
cmb_filterOption.addItemListener(this);
}
if (selectedFilterOpt.getView() == VIEWS_FILTER)
{
mainFrame.setTitle(filterTitle);
- chk_invertFilter.setVisible(true);
- filterResultSet(selectedFilterOpt.getValue());
+ // TDB Query has no invert as yet
+ chk_invertFilter.setVisible(selectedFilterOpt.getQuerySource() instanceof PDBStructureChooserQuerySource);
+
+ if (data!=selectedFilterOpt.getQuerySource() || data.needsRefetch(selectedFilterOpt))
+ {
+ data = selectedFilterOpt.getQuerySource();
+ // rebuild the views completely, since prefs will also change
+ tabRefresh();
+ return;
+ } else {
+ filterResultSet(selectedFilterOpt.getValue());
+ }
}
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
+ PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb.getModel()).getPDBEntryAt(row).getPdbEntry();
+
pdbEntriesToView[count++] = pdbEntry;
SequenceI selectedSeq = (SequenceI) tbl_local_pdb
.getValueAt(row, refSeqColIndex);
public void run()
{
fetchStructuresMetaData();
+ //populateFilterComboBox(true, cachedPDBExists);
+
filterResultSet(
((FilterOption) cmb_filterOption.getSelectedItem())
.getValue());
value = entry.getSequence();
break;
case 1:
- value = entry.getPdbEntry();
+ value = entry.getQualifiedId();
break;
case 2:
value = entry.getPdbEntry().getChainCode() == null ? "_"
this.pdbEntry = pdbEntry;
}
+ public String getQualifiedId()
+ {
+ if (pdbEntry.hasProvider())
+ {
+ return pdbEntry.getProvider()+":"+pdbEntry.getId();
+ }
+ return pdbEntry.toString();
+ }
+
public SequenceI getSequence()
{
return sequence;
git://source.jalview.org / jalview.git / blobdiff