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";
+ /**
+ * warn user if need to fetch more than this many uniprot records at once
+ */
+ 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)
// which FTS engine to use
data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
initDialog();
+
this.ap = ap;
this.selectedSequence = selectedSeq;
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
init();
+
}
/**
Executors.defaultThreadFactory().newThread(new Runnable()
{
+ @Override
public void run()
{
populateSeqsWithoutSourceDBRef();
// 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
/**
* raises dialog for Uniprot fetch followed by 3D beacons search
- * @param ignoreGui - when true, don't ask, just fetch
+ *
+ * @param ignoreGui
+ * - when true, don't ask, just fetch
*/
public void promptForTDBFetch(boolean ignoreGui)
{
{
mainFrame.setEnabled(false);
cmb_filterOption.setEnabled(false);
- progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId);
+ 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;
- lastSelected=(FilterOption) cmb_filterOption.getSelectedItem();
+ 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"));
+ 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);
- } else {
+ 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);
@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);
}
};
};
- if (ignoreGui)
+ 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' TODO: mock should be OK
- JvOptionPane.newOptionDialog(this)
+ 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);
}
/**
discoveredStructuresSet = new LinkedHashSet<>();
HashSet<String> errors = new HashSet<>();
+
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
+
for (SequenceI seq : selectedSequences)
{
+
FTSRestResponse resultList;
try
{
{
getResultTable()
.setModel(data.getTableModel(discoveredStructuresSet));
+
noOfStructuresFound = discoveredStructuresSet.size();
lastDiscoveredStructuresSet = discoveredStructuresSet;
mainFrame.setTitle(MessageManager.formatMessage(
{
Thread filterThread = new Thread(new Runnable()
{
+
@Override
public void run()
{
for (SequenceI seq : selectedSequences)
{
+
FTSRestResponse resultList;
try
{
resultList = data.selectFirstRankedQuery(seq,
discoveredStructuresSet, wantedFields, fieldToFilterBy,
!chk_invertFilter.isSelected());
+
} catch (Exception e)
{
e.printStackTrace();
// 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();
}
}
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(filter);
}
}
+
cmb_filterOption.addItem(
new FilterOption(MessageManager.getString("label.enter_pdb_id"),
"-", VIEWS_ENTER_ID, false, null));
if (canQueryTDB && notQueriedTDBYet)
{
btn_queryTDB.setVisible(true);
+ pnl_queryTDB.setVisible(true);
}
if (cachedPDBExist)
cmb_filterOption.setSelectedItem(cachedOption);
}
}
-
if (selSet > -1)
{
cmb_filterOption.setSelectedIndex(selSet);
// otherwise, record selection
// and update the layout and dialog accordingly
lastSelected = selectedFilterOpt;
+
layout_switchableViews.show(pnl_switchableViews,
selectedFilterOpt.getView());
String filterTitle = mainFrame.getTitle();
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=((ThreeDBStructureChooserQuerySource)data).getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet);
- String pageUrl = row.getModelViewUrl();
+ 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.show(getResultTable(), x, y); }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ popup.show(getResultTable(), x, y);
+ }
});
return true;
}
{
validateSelections();
}
-
private FilterOption lastSelected=null;
/**
* Handles the state change event for the 'filter' combo-box and 'invert'
}
return found;
}
+
/**
* Handles the 'New View' action
*/
{
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)
{
{
PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
.getModel()).getPDBEntryAt(row).getPdbEntry();
+
pdbEntriesToView[count++] = pdbEntry;
SequenceI selectedSeq = (SequenceI) tbl_local_pdb
.getValueAt(row, refSeqColIndex);
}
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.getInstance());
-
- 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
- *
- * @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
* a unique sequence when more than one sequence selection is made.
*/
{
if (selectedSequences != null)
{
+ lbl_loading.setVisible(true);
Thread refreshThread = new Thread(new Runnable()
{
@Override
{
fetchStructuresMetaData();
// populateFilterComboBox(true, cachedPDBExists);
+
filterResultSet(
((FilterOption) cmb_filterOption.getSelectedItem())
.getValue());
+ lbl_loading.setVisible(false);
}
});
refreshThread.start();
*
* @return true if the 3D-Beacons query button will/has been displayed
*/
- public boolean isCanQueryTDB() {
- return canQueryTDB;
+ public boolean isCanQueryTDB()
+ {
+ return canQueryTDB;
}
public boolean isNotQueriedTDBYet()
git://source.jalview.org / jalview.git / blobdiff