import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
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.Console;
import jalview.bin.Jalview;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
public class StructureChooser extends GStructureChooser
implements IProgressIndicator
{
- private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
+ protected static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
/**
- * transient combo box choice for initiating 3db fetch
+ * warn user if need to fetch more than this many uniprot records at once
*/
- private static final String VIEWS_QUERYING_TDB = "QUERY_3DB";
-
+ private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20;
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
List<SequenceI> seqsWithoutSourceDBRef = null;
- private static StructureViewer lastTargetedView = null;
+ protected static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
canQueryTDB = true;
if (needCanonical)
{
- notQueriedTDBYet = false;
+ // triggers display of the 'Query TDB' button
+ notQueriedTDBYet = true;
}
}
};
}
chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+ btn_queryTDB.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ promptForTDBFetch(false);
+ }
+ });
Executors.defaultThreadFactory().newThread(new Runnable()
{
+ @Override
public void run()
{
populateSeqsWithoutSourceDBRef();
updateCurrentView();
}
- private void promptForTDBFetch()
+ /**
+ * raises dialog for Uniprot fetch followed by 3D beacons search
+ *
+ * @param ignoreGui
+ * - when true, don't ask, just fetch
+ */
+ public void promptForTDBFetch(boolean ignoreGui)
{
final long progressId = System.currentTimeMillis();
@Override
public void run()
{
+ mainFrame.setEnabled(false);
+ cmb_filterOption.setEnabled(false);
+ progressBar.setProgressBar(
+ MessageManager.getString("status.searching_3d_beacons"),
+ progressId);
+ btn_queryTDB.setEnabled(false);
// TODO: warn if no accessions discovered
populateSeqsWithoutSourceDBRef();
// redo initial discovery - this time with 3d beacons
// Executors.
- previousWantedFields=null;
-
+ previousWantedFields = null;
+ lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
+ cmb_filterOption.setSelectedItem(null);
+ cachedPDBExists=false; // reset to initial
initialStructureDiscovery();
+ if (!isStructuresDiscovered())
+ {
+ progressBar.setProgressBar(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"),
+ progressId);
+ btn_queryTDB.setToolTipText(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"));
+ btn_queryTDB.setEnabled(false);
+ pnl_queryTDB.setVisible(false);
+ }
+ else
+ {
+ cmb_filterOption.setSelectedIndex(0); // select 'best'
+ btn_queryTDB.setVisible(false);
+ pnl_queryTDB.setVisible(false);
+ progressBar.setProgressBar(null, progressId);
+ }
+ mainFrame.setEnabled(true);
+ cmb_filterOption.setEnabled(true);
}
};
@Override
public void run()
{
+ btn_queryTDB.setEnabled(false);
populateSeqsWithoutSourceDBRef();
final int y = seqsWithoutSourceDBRef.size();
dbRefFetcher.addListener(afterDbRefFetch);
// ideally this would also gracefully run with callbacks
dbRefFetcher.fetchDBRefs(true);
- } else {
+ }
+ else
+ {
// call finished action directly
afterDbRefFetch.finished();
}
}
};
- final Runnable revertview = new Runnable() {
- public void run() {
- if (lastSelected!=null) {
+ final Runnable revertview = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (lastSelected != null)
+ {
cmb_filterOption.setSelectedItem(lastSelected);
}
};
};
+ int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
+ THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
+ Console.debug("Using Uniprot fetch threshold of " + threshold);
+ if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
+ {
+ Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+ return;
+ }
// need cancel and no to result in the discoverPDB action - mocked is
- // 'cancel'
- JvOptionPane.newOptionDialog(this)
+ // 'cancel' TODO: mock should be OK
+ StructureChooser thisSC = this;
+ JvOptionPane.newOptionDialog(thisSC.getFrame())
.setResponseHandler(JvOptionPane.OK_OPTION,
discoverCanonicalDBrefs)
.setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview)
null, new Object[]
{ MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") },
- MessageManager.getString("action.ok"));
+ MessageManager.getString("action.ok"), false);
}
/**
*/
private void discoverStructureViews()
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
targetView.removeAllItems();
if (lastTargetedView != null && !lastTargetedView.isVisible())
lastTargetedView = null;
}
int linkedViewsAt = 0;
- for (StructureViewerBase view : Desktop.instance
+ for (StructureViewerBase view : Desktop.getInstance()
.getStructureViewers(null, null))
{
StructureViewer viewHandler = (lastTargetedView != null
// StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(
MessageManager.formatMessage("label.select_pdb_file_for",
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
"-", VIEWS_FROM_FILE, false, null));
if (canQueryTDB && notQueriedTDBYet)
{
- FilterOption queryTDBOption = new FilterOption(
- MessageManager.getString("label.search_3dbeacons"), "-",
- VIEWS_QUERYING_TDB, false, null);
- cmb_filterOption.addItem(queryTDBOption);
+ btn_queryTDB.setVisible(true);
+ pnl_queryTDB.setVisible(true);
}
if (cachedPDBExist)
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
- // first check if we need to rebuild dialog
- if (selectedFilterOpt.getView() == VIEWS_QUERYING_TDB)
- {
- promptForTDBFetch();
- return;
- }
if (lastSelected == selectedFilterOpt)
{
// don't need to do anything, probably
}
@Override
- protected boolean showPopupFor(int selectedRow)
+ protected boolean showPopupFor(int selectedRow, int x, int y)
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER && data instanceof ThreeDBStructureChooserQuerySource)
+ if (currentView == VIEWS_FILTER
+ && data instanceof ThreeDBStructureChooserQuerySource)
{
- TDB_FTSData row=null;
-
- int i=1;
- for (FTSData el:discoveredStructuresSet) {
- if (i==selectedRow) {
- row = (TDB_FTSData) el;
- break;
- }
- i++;
- }
- String pageUrl = row.getModelViewUrl();
- JMenu popup = new JMenu("3D Beacons");
+ TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
+ .getFTSDataFor(getResultTable(), selectedRow,
+ discoveredStructuresSet);
+ String pageUrl = row.getModelViewUrl();
+ JPopupMenu popup = new JPopupMenu("3D Beacons");
JMenuItem viewUrl = new JMenuItem("View model web page");
- viewUrl.addActionListener(
- new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- Desktop.showUrl(pageUrl);
- }
- }
- );
+ viewUrl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(pageUrl);
+ }
+ });
popup.add(viewUrl);
- SwingUtilities.invokeLater(new Runnable() {
- public void run() { popup.setVisible(true); }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ popup.show(getResultTable(), x, y);
+ }
});
return true;
}
{
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
-
+ final StructureViewer theViewer = getTargetedStructureViewer(ssm);
+ boolean superimpose = chk_superpose.isSelected();
final int preferredHeight = pnl_filter.getHeight();
Runnable viewStruc = new Runnable()
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_ENTER_ID)
{
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
- new SequenceI[]
- { selectedSequence });
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ new SequenceI[]
+ { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
else if (currentView == VIEWS_FROM_FILE)
{
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
-
- sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
- ap, new SequenceI[]
- { selectedSequence });
+ PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true);
+
+ sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
+ new SequenceI[] { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
SwingUtilities.invokeLater(new Runnable()
{
}
/**
- * Adds PDB structures to a new or existing structure viewer
+ * Creates or updates a structure view with given structures
*
* @param ssm
* @param pdbEntriesToView
* @param alignPanel
* @param sequences
- * @return
- */
- 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 theViewer = getTargetedStructureViewer(ssm);
- boolean superimpose = chk_superpose.isSelected();
- theViewer.setSuperpose(superimpose);
-
- /*
- * remember user's choice of superimpose or not
- */
- Cache.setProperty(AUTOSUPERIMPOSE,
- Boolean.valueOf(superimpose).toString());
-
- 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().isEmpty())
- {
- 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 = seqsWithoutSourceDBRef
- .toArray(new SequenceI[y]);
- 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);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
- }
- else
- {
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()), progressId);
- theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
- setProgressBar(null, progressId);
- // remember the last viewer we used...
- lastTargetedView = theViewer;
- return theViewer;
- }
+ *
/**
* Populates the combo-box used in associating manually fetched structures to
{
if (selectedSequences != null)
{
+ lbl_loading.setVisible(true);
Thread refreshThread = new Thread(new Runnable()
{
@Override
filterResultSet(
((FilterOption) cmb_filterOption.getSelectedItem())
.getValue());
+ lbl_loading.setVisible(false);
}
});
refreshThread.start();
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(long id, IProgressIndicatorHandler handler)
&& mainFrame.isVisible()
&& cmb_filterOption.getSelectedItem() != null;
}
+ /**
+ *
+ * @return true if the 3D-Beacons query button will/has been displayed
+ */
+ public boolean isCanQueryTDB()
+ {
+ return canQueryTDB;
+ }
+
+ public boolean isNotQueriedTDBYet()
+ {
+ return notQueriedTDBYet;
+ }
}
git://source.jalview.org / jalview.git / blobdiff