package jalview.gui;
+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.concurrent.Executors;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
+import javax.swing.table.AbstractTableModel;
+
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.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.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.DBRefFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
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.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
*
private boolean cachedPDBExists;
+ private Collection<FTSData> lastDiscoveredStructuresSet;
+
private static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
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()
+ 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
+ // check which FTS engine to use
+ data = StructureChooserQuerySource
+ .getQuerySourceFor(selectedSequences);
+
+ // ensure a filter option is in force for search
+ populateFilterComboBox(true, cachedPDBExists);
+
+ // 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,
+ progressBar, new DbSourceProxy[]
+ { new jalview.ws.dbsources.Uniprot() },
+ null, false);
+
+ dbRefFetcher.fetchDBRefs(true);
+
+ setProgressBar("Fetch complete.", progressId); // todo i18n
+
+ Executors.defaultThreadFactory().newThread(discoverPDBStructures).start();
+ }
+ };
+
+ Executors.defaultThreadFactory().newThread(new Runnable()
+ {
+ public void run()
+ {
+
+ for (SequenceI seq : selectedSequences)
+ {
+ if (seq.isProtein())
+ {
+ int dbRef = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (dbRef < 0)
+ {
+ if (seq.getAllPDBEntries()==null && seq.getAllPDBEntries().size()==0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ }
+ }
+ }
+ // retrieve database refs for protein sequences
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ // need cancel and no to result in the discoverPDB action - mocked is 'cancel'
+ JvOptionPane.newOptionDialog(Desktop.getDesktop())
+ .setResponseHandler(JvOptionPane.OK_OPTION, discoverCanonicalDBrefs)
+ .setResponseHandler(JvOptionPane.CANCEL_OPTION, discoverPDBStructures)
+ .setResponseHandler(JvOptionPane.NO_OPTION, 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()
{
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)
{
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;
data.setDocFieldPrefs(newPrefs);
}
+
+ /**
+ *
+ * @return true when all initialisation threads have finished and dialog is visible
+ */
+ public boolean isDialogVisible()
+ {
+ return mainFrame != null && data != null && cmb_filterOption != null
+ && mainFrame.isVisible()
+ && cmb_filterOption.getSelectedItem() != null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff