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 javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
/**
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()
fetchStructuresMetaData();
// 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
*
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
- discoveredStructuresSet = new LinkedHashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ discoveredStructuresSet = new LinkedHashSet<>();
+ HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
FTSRestRequest pdbRequest = new FTSRestRequest();
public void loadLocalCachedPDBEntries()
{
- ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
+ ArrayList<CachedPDB> entries = new ArrayList<>();
for (SequenceI seq : selectedSequences)
{
if (seq.getDatasetSequence() != null
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- Set<String> seqRefs = new LinkedHashSet<String>();
+ Set<String> seqRefs = new LinkedHashSet<>();
if (seq.getAllPDBEntries() != null
&& queryBuilder.length() < MAX_QLENGTH)
lbl_loading.setVisible(true);
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
- Collection<FTSData> filteredResponse = new HashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ Collection<FTSData> filteredResponse = new HashSet<>();
+ HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
- Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(FTSRestResponse
* structures
*/
protected void populateFilterComboBox(boolean haveData,
- boolean cachedPDBExists)
+ boolean cachedPDBExist)
{
/*
* temporarily suspend the change listener behaviour
cmb_filterOption.removeAllItems();
if (haveData)
{
- cmb_filterOption.addItem(new FilterOption("Best Quality",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_quality"),
"overall_quality", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Best Resolution",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.best_resolution"),
"resolution", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_protein_chain"),
"number_of_protein_chains", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_bound_molecules"),
"number_of_bound_molecules", VIEWS_FILTER, false));
- cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
+ cmb_filterOption.addItem(new FilterOption(
+ MessageManager.getString("label.most_polymer_residues"),
"number_of_polymer_residues", VIEWS_FILTER, true));
}
cmb_filterOption.addItem(
- new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false));
+ new FilterOption(MessageManager.getString("label.enter_pdb_id"),
+ "-", VIEWS_ENTER_ID, false));
cmb_filterOption.addItem(
- new FilterOption("From File", "-", VIEWS_FROM_FILE, false));
+ new FilterOption(MessageManager.getString("label.from_file"),
+ "-", VIEWS_FROM_FILE, false));
- if (cachedPDBExists)
+ if (cachedPDBExist)
{
- FilterOption cachedOption = new FilterOption("Cached PDB Entries",
+ FilterOption cachedOption = new FilterOption(
+ MessageManager.getString("label.cached_structures"),
"-", VIEWS_LOCAL_PDB, false);
cmb_filterOption.addItem(cachedOption);
cmb_filterOption.setSelectedItem(cachedOption);
}
/**
+ * 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;
+
+ 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()
{
- final long progressSessionId = System.currentTimeMillis();
+ 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();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
- new Thread(new Runnable()
+
+ 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 = getResultTable().getColumn("PDB Id")
+ int pdbIdColIndex = restable.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
+ int refSeqColIndex = restable.getColumn("Ref Sequence")
.getModelIndex();
- int[] selectedRows = getResultTable().getSelectedRows();
+ int[] selectedRows = restable.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
- List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- String pdbIdStr = getResultTable()
+ String pdbIdStr = restable
.getValueAt(row, pdbIdColIndex).toString();
- SequenceI selectedSeq = (SequenceI) getResultTable()
+ SequenceI selectedSeq = (SequenceI) restable
.getValueAt(row, refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
+
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
.getModelIndex();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
- List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
{
{
selectedSequence = userSelectedSeq;
}
-
String pdbIdStr = txt_search.getText();
PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[]
{ selectedSequence });
}
DataSourceType.FILE, selectedSequence, true,
Desktop.instance);
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ sViewer = launchStructureViewer(
+ ssm, new PDBEntry[]
+ { fileEntry }, ap,
new SequenceI[]
{ selectedSequence });
}
- closeAction(preferredHeight);
+ 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)
+ {
+
+ }
}
- }).start();
+ }
}
private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
return foundEntry;
}
- private void launchStructureViewer(StructureSelectionManager ssm,
+ /**
+ * @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)
{
- ssm.setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"));
- final StructureViewer sViewer = new StructureViewer(ssm);
+ 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<SequenceI>();
+ 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
if (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_dbrefs_for_sequences_without_valid_refs",
- y));
+ 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)
{
- ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
- for (SequenceI seq : sequences)
- {
- seqsMap.add(new SequenceI[] { seq });
- }
- SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.getString(
- "status.fetching_3d_structures_for_selected_entries"));
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
+ setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"),
+ progressId);
+ sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
}
else
{
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
+ pdbEntriesToView[0].getId()),progressId);
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
+ setProgressBar(null, progressId);
+ // remember the last viewer we used...
+ lastTargetedView = sViewer;
+ return sViewer;
}
/**
String searchTerm = txt_search.getText().toLowerCase();
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ List<FTSDataColumnI> wantedFields = new ArrayList<>();
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
public PDBEntryTableModel(List<CachedPDB> pdbEntries)
{
- this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
+ this.pdbEntries = new ArrayList<>(pdbEntries);
}
@Override
{
return progressBar.operationInProgress();
}
+
+ public JalviewStructureDisplayI getOpenedStructureViewer()
+ {
+ return sViewer == null ? null : sViewer.sview;
+ }
}
git://source.jalview.org / jalview.git / blobdiff